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RIKEN BioResource Research Center - Japan Collection of Microorganisms
JCM Mail News (2025.03.13)
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RIKEN BioResource Research Center - Japan Collection of Microorganisms
(JCM) is pleased to update you with the latest information.
======= Contents =====================================================
- Special topic: Gut microbes isolated by the spore germination
induction method
- EMALiMB ver3.0, the MALDI-TOF MS reference library of various
microbial strains released
- "JCM BLAST Search" released
- Newly cataloged strains (2024.11.01 - 2025.02.28)
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Special topic: Gut microbes isolated by the spore germination
induction method
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Our research aims to isolate unidentified and unclassified bacteria
from the human gut and to develop bioresources from the perspective of
securing microbial resources and their utilization. Especially, gut
microbes are relevant to human physiological functions and various
diseases, and are of critical importance in various industrial fields
including drug development; for example, Waltera acetigignens
(JCM 36210), Anaerostipes caccae (JCM 13470T) and Anaerostipes hominis
(JCM 32275T), which have been suggested to form spores, produce
butyric acid. Therefore, it is expected that they will be further
investigated as probiotics in the future. Above-mentioned bacterial
species are known to form spores to protect their cells from stresses
such as heat and acidity and to become resting forms. Cultivation
requires stimuli to induce germination, which is known to be difficult
due to the diversity of germination factors among bacterial species.
Therefore, we introduced a new culture method to induce spore
germination by sterilizing liquid culture medium from fecal material
and adding it to fecal material.
As a result, Bacterial species of the genera Anaerobutyricum,
Roseburia, Ruminococcus, and Waltera were isolated which are expected
to be probiotics. In addition, a number of bacterial species that are
expected to be new species were also isolated. The culture method to
induce spore germination as described above is expected to not only
contribute to the isolation of bacteria, but also to a better
understanding of the original potential of bacteria that cannot be
demonstrated in a resting forms.
References
Sakamoto et al. 2024. Isolation and characterization of a new Waltera
species and reclassification of Brotolimicola acetigignens Hitch et al.
2022 as Waltera acetigignens comb. nov.
Int. J. Syst. Evol. Microbiol., 74: 006381.
DOI: 10.1099/ijsem.0.006381
Kadowaki et al. 2023. Spore-forming properties and enhanced oxygen
tolerance of butyrate-producing Anaerostipes spp.
Anaerobe., 82: 102752
DOI: 10.1016/j.anaerobe.2023.102752
Atsushi Hisatomi Ph.D.
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EMALiMB ver3.0, the MALDI-TOF MS reference library of various
microbial strains released
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JCM, IFM, GTC, and NEKKEN* established a new MALDI-TOF MS reference
library 'EMALiMB' (Expanded MALDI-TOF MS Library for MALDI Biotyper®)
for various microbial strains, and have released the ver3.0. For more
details, please visit the webpage below.
https://www.jcm.riken.jp/NBRP_MALDI-TOF_MS/nbrp_maldi_tof_ms_ref_lib_e.html
EMALiMB_NBRP_Library_ver3.0 provides 2,000 data of the JCM + IFM
strains (eukaryotic microbes), ca. 1,140 data of the JCM + GTC strains
(prokaryotes), and 14 data of the NEKKEN strains (including Trypanosoma),
etc. In this current version, the MALDI-TOF MS data of anaerobes
including lactic acid bacteria and intestinal bacteria are available.
Please note that the ver3.0 includes the data from the ver2.0.
This project was supported by the FY2020-2021 Fundamental Technology
Upgrading Program of National BioResource Project (NBRP) of the MEXT,
Japan, and we have been adding MALDI-TOF MS data in the current
version of the library. The microbial strains used in this project are
available from JCM, IFM, GTC, and NEKKEN.
* JCM: Japan Collection of Microorganisms, RIKEN BioResource
Research Center
IFM: Medical Mycology Research Center, Chiba University
GTC: Center for Conservation of Microbial Genetic Resource, Gifu
University
NEKKEN: Institute of Tropical Medicine, Nagasaki University
Rikiya Endoh, curator of yeasts and yeast-like alga
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"JCM BLAST Search" released
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"JCM BLAST search" is now available. This feature allows you to search
for JCM strains (or equivalent strains) with genome sequences
homologous to your query sequence. At the present version, only
prokaryotic strains are included.
JCM BLAST search
https://www.jcm.riken.jp/JCM/jcmblast/en/
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Newly cataloged strains (2024.11.01 - 2025.02.28)
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Bacteria
"Achromobacter cholinophagum" JCM 20645
Amycolatopsis melonis JCM 35654 Type strain
Anaerobaca lacustris JCM 39238 Type strain
Aureispira anguillae JCM 35024 Type strain
Bacillus suaedaesalsae JCM 34525 Type strain
Bengtsoniella intestinalis JCM 35770 Type strain
Bifidobacterium apicola JCM 37002 Type strain
Bifidobacterium favimelis JCM 36315 Type strain
Bifidobacterium favimelis JCM 36316
"Chloracidobacterium validum" JCM 39534 Proposed type strain
Chromobacterium sp. JCM 20646
Chromobacterium sp. JCM 20647
Clostridium lapidicellarium JCM 36532 Type strain
Clostridium moutaii JCM 36530 Type strain
Comamonas halotolerans JCM 35999 Type strain
Crenobacter oryzisoli JCM 36468 Type strain
Desulfosporosinus paludis JCM 39521 Type strain
Desulfovibrio falkowii JCM 36128 Type strain
Enterobacter chinensis JCM 35826 Type strain
Enterobacter rongchengensis JCM 36189 Type strain
Faecalibacterium wellingii JCM 39548 Type strain
"Fervidibacter sacchari" JCM 39283 Proposed type strain
Flavivirga abyssicola JCM 36477 Type strain
Flavobacterium flavipigmentatum JCM 34198 Type strain
Flavobacterium lipolyticum JCM 34199 Type strain
Flavobacterium pisciphilum JCM 34197 Type strain
Flavobacterium piscisymbiosum JCM 34194 Type strain
Geothrix campi JCM 39331 Type strain
Halalkalibacter flavus JCM 36285 Type strain
Halalkalibacter lacteus JCM 36286 Type strain
Halomonas sp. JCM 20648
"Helicobacter felistomachi" JCM 39513 Proposed type strain
"Helicobacter gastrocanis" JCM 39159 Proposed type strain
"Helicobacter gastrofelis" JCM 39160 Proposed type strain
Hominibacterium faecale JCM 34755 Type strain
Hyalangium rubrum JCM 39263 Type strain
Hydrogenimonas leucolamina JCM 39184 Type strain
Janibacter alittae JCM 36706 Type strain
Kosakonia calanthes JCM 36393 Type strain
Lacticaseibacillus jixiensis JCM 36999 Type strain
Lapidilactobacillus salsurivasis JCM 36613 Type strain
Lentilactobacillus terminaliae JCM 35081 Type strain
Litchfieldia suaedae JCM 34524 Type strain
Mediterraneibacter flintii JCM 36130 Type strain
Microbispora maris JCM 36778 Type strain
Minisyncoccus archaeiphilus JCM 39522 Type strain
Novacetimonas hansenii JCM 37641
Owariibacterium komagatae JCM 36131 Type strain
Paenalkalicoccus suaedae JCM 33851 Type strain
"Parabacteroides absconsus" JCM 35468 Proposed type strain
Paracoccus benzoatiresistens JCM 35642 Type strain
"Parasalinivibrio latis" JCM 36283 Proposed type strain
Pleionea litopenaei JCM 36490 Type strain
Porphyromonas miyakawae JCM 36129 Type strain
Pseudomonas machongensis JCM 36318 Type strain
"Robertmurraya mangrovi" JCM 36937 Proposed type strain
Roseomonas cutis JCM 34968 Type strain
Rosettibacter firmus JCM 39243 Type strain
Rosettibacter primus JCM 39244 Type strain
Secundilactobacillus muriivasis JCM 36612 Type strain
Segatella asaccharophila JCM 37351 Type strain
Sporosarcina jeotgali JCM 36032 Type strain
Sporosarcina oncorhynchi JCM 36031 Type strain
Sporosarcina trichiuri JCM 36034 Type strain
Stenotrophomonas capsici JCM 36317 Type strain
Streptococcus parapneumoniae JCM 36068 Type strain
Streptococcus parasalivarius JCM 36614 Type strain
Streptomyces avermitilis JCM 37479
Streptomyces avermitilis JCM 37480
Streptomyces avermitilis JCM 37481
Streptomyces avermitilis JCM 37482
Streptomyces avermitilis JCM 37483
Streptomyces avermitilis JCM 37484
Streptomyces avermitilis JCM 37485
Streptomyces avermitilis JCM 37486
Terrimonas pollutisoli JCM 36215 Type strain
Thalassospira aquimaris JCM 35895 Type strain
Thalassotalea psychrophila JCM 33807 Type strain
"Thermodesulfovibrio autotrophicus" JCM 39445 Proposed type strain
"Thermodesulfovibrio obliviosus" JCM 39444 Proposed type strain
Virgibacillus sp. JCM 20649
Winogradskyella marincola JCM 35950 Type strain
Xanthocytophaga agilis JCM 35374 Type strain
Xanthocytophaga flava JCM 35375 Type strain
Xanthocytophaga flava JCM 35376
Xanthocytophaga flava JCM 35377
Yoonia algicola JCM 35790 Type strain
Yoonia phaeophyticola JCM 35751 Type strain
Yoonia rhodophyticola JCM 35753 Type strain
Archaea
"Halalkalicoccus ordinarius" JCM 34143 Proposed type strain
"Halalkalicoccus salilacus" JCM 35075
"Halalkalicoccus salilacus" JCM 36674 Proposed type strain
"Haloarcula brevis" JCM 36146 Proposed type strain
Haloarcula ordinaria JCM 30035 Type strain
"Haloarcula regularis" JCM 36149 Proposed type strain
"Haloarcula sediminis" JCM 36675 Proposed type strain
"Halobellus rubicundus" JCM 36642 Proposed type strain
"Halovalidus salilacus" JCM 35096 Proposed type strain
"Natronococcus wangiae" JCM 33734 Proposed type strain
"Natronococcus zhouii" JCM 34160 Proposed type strain
"Natronorarus salvus" JCM 34309 Proposed type strain
"Nitrosocosmicus oleophilus" JCM 31642
Oxyplasma meridianum JCM 36570 Type strain
Fungi
Acaromyces sp. JCM 36089
Apiotrichum coprophilum JCM 24545
Apiotrichum scarabaeorum JCM 24548
Barnettozyma californica JCM 24546
Bauerozyma artemisiae JCM 36118 Type strain
Boekhoutia foliicola JCM 36090 Type strain
Buckleyzyma pseudoaurantiaca JCM 36091 Type strain
Candida boidinii JCM 28611
Candida intermedia JCM 24530
Candida tumulicola JCM 28220
Carlosrosaea betulae JCM 36094 Type strain
Carlosrosaea rhododendri JCM 36092 Type strain
Carlosrosaea yunnanensis JCM 36093 Type strain
Chionobium takahashii JCM 39510 ex-holotype strain
Colacogloea pararetinophila JCM 35724 Type strain
Cystastrum sp. JCM 24567
Cystobasidium calyptogenae JCM 23224
Cystobasidium calyptogenae JCM 23225
Cystobasidium cunninghamiae JCM 35968 Type strain
Cystobasidium minutum JCM 23222
Cystobasidium minutum JCM 24543
Derxomyces motuoensis JCM 36096 Type strain
Derxomyces paracylindricus JCM 36097 Type strain
Derxomyces paracylindricus JCM 36098
Exobasidium lijiangense JCM 36100 Type strain
Fellomyces sp. JCM 24549
Fibulobasidium sp. JCM 36101
Fonsecazyma sp. JCM 36103
Geotrichum dehoogii JCM 35432 Type strain
Geotrichum fujianense JCM 36366 Type strain
Geotrichum maricola JCM 35433 Type strain
Geotrichum reessii JCM 3680
Geotrichum sinensis JCM 36365 Type strain
Geotrichum smithiae JCM 35056 Type strain
Halobasidium phyllophilum JCM 35974 Type strain
Hannaella artemisiae JCM 36105 Type strain
Hannaella luteola JCM 24534
Hannaella taiwanensis JCM 24560
Hannaella theobromatis JCM 36106
Holtermannia pseudosaccardoi JCM 36107 Type strain
Kockovaella cariosiligni JCM 36108 Type strain
Kwoniella bestiolae JCM 24531
Kwoniella bestiolae JCM 24532
Kwoniella hippophaes JCM 36111 Type strain
Kwoniella lonicerae JCM 36110 Type strain
Litoriozyma hainanensis JCM 35969 Type strain
Meira sp. JCM 36112
Meredithblackwellia sp. JCM 24547
Meyerozyma caribbica JCM 28224
Meyerozyma caribbica JCM 28227
Meyerozyma guilliermondii JCM 28205
Meyerozyma guilliermondii JCM 28207
Meyerozyma guilliermondii JCM 28212
Meyerozyma guilliermondii JCM 28213
Meyerozyma guilliermondii JCM 28214
Meyerozyma guilliermondii JCM 28215
Meyerozyma guilliermondii JCM 28216
Meyerozyma guilliermondii JCM 28217
Meyerozyma guilliermondii JCM 28218
Meyerozyma guilliermondii JCM 28219
Microsporomyces betulae JCM 36119 Type strain
Microsporomyces foliicola JCM 36099 Type strain
Mrakia pini JCM 35971 Type strain
Myxozyma sp. JCM 28597
Naematelia sp. JCM 35970
Papiliotrema castaneae JCM 35973 Type strain
Papiliotrema flavescens JCM 24533
Papiliotrema leoncinii JCM 24551
Papiliotrema sp. JCM 24553
Papiliotrema sp. JCM 35972
Papiliotrema taeanensis JCM 24550
Phaeotremella pini JCM 36120 Type strain
Phaffia rhododendri JCM 36121 Type strain
Pichia membranifaciens JCM 28206
Pichia membranifaciens JCM 28208
Pichia membranifaciens JCM 28209
Pichia membranifaciens JCM 28211
Piskurozyma cuscutae JCM 36122 Type strain
Piskurozyma liliaceifoliae JCM 36123 Type strain
Piskurozyma linzhiensis JCM 36157 Type strain
Piskurozyma nanyiensis JCM 36124 Type strain
Pseudohyphozyma sanghuangpori JCM 36125 Type strain
Pseudotremella hippophaes JCM 36126 Type strain
Pseudotremella sp. JCM 24557
Pseudozyma alboarmeniaca JCM 12454 Type strain
Pseudozyma crassa JCM 12455 Type strain
Pseudozyma siamensis JCM 12456 Type strain
Rhodotorula paludigena JCM 24539
Rhodotorula sphaerocarpa JCM 24541
Rhynchogastrema sp. JCM 24552
Saccharomyces cerevisiae JCM 37081
Saccharomyces cerevisiae JCM 37082
Saccharomyces cerevisiae JCM 37083
Saccharomyces cerevisiae JCM 37084
Saccharomyces cerevisiae JCM 37085
Saitozyma sp. JCM 36127
Slooffia terricola JCM 36158 Type strain
Solicoccozyma terricola JCM 24528
Starmerella fangiana JCM 36911
Starmerella fangiana JCM 36912 Type strain
Starmerella fangiana JCM 36913
Takashimella corticis JCM 35967 Type strain
Teunia chimonanthi JCM 36160 Type strain
Teunia heritierae JCM 36161 Type strain
Teunia myricariae JCM 36159 Type strain
Teunia parabetulicola JCM 36109 Type strain
Teunia quercus JCM 36162 Type strain
Teunia rhododendri JCM 36164 Type strain
Vanrija silvicola JCM 36095 Type strain
Vishniacozyma catalpae JCM 36170 Type strain
Vishniacozyma marinae JCM 36165 Type strain
Vishniacozyma paravictoriae JCM 36169 Type strain
Vishniacozyma pini JCM 36166 Type strain
Vishniacozyma pyri JCM 36168 Type strain
Vishniacozyma sinopodophylli JCM 36167 Type strain
Vishniacozyma sp. JCM 24558
Wickerhamomyces anomalus JCM 24538
Xenoacremonium sp. JCM 36629
Yamadazyma olivae JCM 28626
Yamadazyma thunbergiae JCM 24746
Yamadazyma thunbergiae JCM 24748
Yamadazyma thunbergiae JCM 24755
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Microbe Division / Japan Collection of Microorganisms
RIKEN BioResource Research Center
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2025.03.13
