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RIKEN BioResource Research Center - Japan Collection of Microorganisms
JCM Mail News (2026.03.19)
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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: A systematic overview of CO2-fixing microorganisms
in the JCM collection
- Revision of Distribution Fees for Bioresources in RIKEN BRC
- Newly cataloged strains (2025.12.01 - 2026.02.28)
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Special topic: A systematic overview of CO2-fixing microorganisms
in the JCM collection
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To deepen our understanding of microorganisms and to utilize them
effectively as biological resources, it is important to integrate
genome information with cultivation data.
To this end, we examined the presence of Calvin–Benson–Bassham (CBB)
cycle–related genes and CO2 fixation capabilities among approximately
6,700 genome-sequenced microbial strains maintained in the Japan
Collection of Microorganisms (JCM) [Nishihara A, et al. 2026]. Our
analysis revealed a lack of experimental confirmation of the ability
to fix CO2 in many cultured microbial strains.
The analysis found that 147 genera (approximately 300 strains)
harbored CBB cycle–related genes. Among these, CO2 fixation has been
reported in 74 genera. In contrast, the remaining 73 genera consist
of strains for which CO2 fixation capability has not yet been reported
in the literature or has not yet been verified experimentally.
In particular, several lineages within Actinomycetota
(Streptosporangiales) and Deinococcota (Thermales) contain strains
that may possess CO2 fixation potential but their autotrophic growth
has not yet been reported.
Therefore, we systematically organized the data based on literature
surveys and genome analyses by integrating gene information with
cultivation conditions, including oxygen concentration, temperature,
pH, energy sources (electron donors), and isolation environments.
The dataset we put together gives a foundation for research on CO2
fixation using microbial resources from JCM.
CO2 fixation, the process by which carbon dioxide is incorporated
into organic compounds, is a fundamental biological activity that
supports global biogeochemical cycles. The CBB cycle is one of the
most widespread mechanisms of CO2 fixation and is estimated to account
for approximately 95% of carbon fixation on Earth. With growing
interest in technologies that utilize CO2 as a resource,
microorganisms possessing the CBB cycle are attracting attention not
only for understanding the carbon cycle but also for potential
applications in environmentally sustainable production processes and
bio-manufacturing.
Several representative microorganisms capable of CO2 fixation
via the CBB cycle are listed below.
•Cupriavidus necator (e.g., JCM 36303)
Formerly known as Ralstonia eutropha, Wautersia eutropha, or
Alcaligenes eutrophus.
This hydrogen-oxidizing bacterium is a well-established model organism
and is widely used in industrial applications such as the production
of the bioplastic polyhydroxyalkanoate (PHA) [e.g., Pohlmann A, et al.
2006]. Nine strains, including the type strain, are preserved in the JCM.
• Acidithiobacillus thiooxidans (e.g., JCM 3867)
Formerly known as Thiobacillus thiooxidans.
This species oxidizes sulfur and sulfur compounds in acidic
environments. It is utilized in bioleaching, a technology that uses
microorganisms to recover metals from ores [e.g., Wang J, et al. 2014].
Five strains, including the type strain, are preserved in the JCM.
• Hydrogenovibrio marinus (JCM 7688)
A hydrogen-oxidizing autotrophic bacterium isolated from marine
environments. It exhibits high oxygen tolerance and has been reported
to grow under relatively high oxygen concentrations (up to 40%)
[Nishihara H, et al. 1991]. This organism possesses two types of
RuBisCO enzyme which involved in the CBB cycle.
• Cereibacter sphaeroides (JCM 6121)
Formerly known as Rhodobacter sphaeroides or Rhodopseudomonas
sphaeroides. This purple non-sulfur bacterium is a widely used model
organism in studies of photosynthesis and the CBB cycle and possesses
two forms of RuBisCO enzyme [e.g.,Tabita FR. 1988].
References
Nishihara A, et al. 2026.
Exploring the diversity and metabolic potential of CO2 fixation
mediated by RubisCO in prokaryotes in the Japan Collection of
Microorganisms.
Microbes and Environments 41: ME25035.
DOI: 10.1264/jsme2.ME25035
Pohlmann A, et al. 2006.
Genome sequence of the bioplastic-producing "Knallgas" bacterium
Ralstonia eutropha H16.
Nature Biotechnology 24: 1257–1262.
DOI: 10.1038/nbt1244
Wang J, et al. 2014.
Bioleaching of low-grade copper sulfide ores by Acidithiobacillus
ferrooxidans and Acidithiobacillus thiooxidans.
Journal of Central South University 21: 728–734.
DOI: 10.1007/s11771-014-1995-3
Nishihara H, et al. 1991.
Growth characteristics and high cell-density cultivation of a marine
obligately chemolithoautotrophic hydrogen-oxidizing bacterium
Hydrogenovibrio marinus strain MH-110 under a continuous gas-flow system.
Journal of Fermentation and Bioengineering 72: 358–361.
DOI: 10.1016/0922-338X(91)90087-W
Tabita FR. 1988.
Molecular and cellular regulation of autotrophic carbon dioxide
fixation in microorganisms.
Microbiological Reviews 52: 155–189.
DOI: 10.1128/mr.52.2.155-189.1988
Arisa Nishihara, Ph.D.
Postdoctoral Researcher
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Revision of Distribution Fees for Bioresources in RIKEN BRC
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RIKEN BioResource Research Center (BRC) is a non-profit institution
and only requires users to pay the minimum costs for the actual
preparation and handling of resources for distribution.
Due to the rising costs of labor and raw materials, we have decided to
revise our distribution fees.
The revised distribution fees will apply to all orders for
bioresources on or after Wednesday, April 1, 2026.
We deeply appreciate your understanding and cooperation, and we look
forward to receiving your requests for bioresources.
https://web.brc.riken.jp/en/archives/news/20260210_01
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Newly cataloged strains (2025.12.01 - 2026.02.28)
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Bacteria
Acetobacterium sp. JCM 14819
Acidaminobacterium chupaoyuni JCM 37290 Type strain
Agarivorans sediminis JCM 35392 Type strain
Agromyces excoecariae JCM 34940 Type strain
Alicyclobacillus sp. JCM 15091
Allocoprococcus comes JCM 37939 Type strain
Allocoprococcus similis JCM 37173 Type strain
"Ammoniphilus soli" JCM 37210 Proposed type strain
"Anoxybacillus tunisiense" JCM 15468
Apilactobacillus pseudapinorum JCM 37175 Type strain
Aquimarina rhabdastrellae JCM 37598 Type strain
Asticcacaulis carbonis JCM 34539 Type strain
Aurantiacibacter sediminis JCM 33995 Type strain
"Bacillus spongicola" JCM 36756 Proposed type strain
Bartonella eidoli JCM 36791 Type strain
Bartonella numerosa JCM 36790 Type strain
Bartonella occidentalis JCM 36789 Type strain
Bartonella propinqua JCM 36786 Type strain
Bartonella rhinolophi JCM 36787 Type strain
Bartonella vaga JCM 36788 Type strain
"Caldiclava thermospodii" JCM 16306
"Cellulophaga omnivescoria" JCM 32108 Proposed type strain
Chelatococcus sp. JCM 37729
Chitinirhabdus sediminis JCM 37906 Type strain
Chryseobacterium chendengshani JCM 33877 Type strain
Chryseobacterium subflavum JCM 33868 Type strain
"Clostridium minutum" JCM 14820
"Clostridium paridis" JCM 34646 Proposed type strain
"Clostridium rhizosphaerae" JCM 34845 Proposed type strain
Clostridium sp. JCM 16182
Clostridium sp. JCM 16314
Clostridium sp. JCM 16807
Clostridium sp. JCM 16808
"Clostridium yunnanense" JCM 34644 Proposed type strain
Coprococcus eutactus JCM 37940 Type strain
Croceiramulus getboli JCM 36479 Type strain
"Curtobacterium pomorum" JCM 37513 Proposed type strain
Dysgonomonas reticulitermitis JCM 35194 Type strain
Faecalimonas hominis JCM 37172 Type strain
Faecalimonas mobilis JCM 37798 Type strain
Faecalimonas nexilis JCM 37525
Fervidobacterium sp. JCM 15582
"Fervidobacterium tianchisum" JCM 14752
Flagellimonas rhodophyticola JCM 37802 Type strain
Flagellimonas ulvae JCM 37803 Type strain
"Flavobacterium agrisoli" JCM 34302 Proposed type strain
Hominimerdicola intestinalis JCM 36633 Type strain
Indolivaga alginatilytica JCM 38120 Type strain
Kocuria kalidii JCM 37381 Type strain
Kocuria rhizosphaerae JCM 37379 Type strain
Kocuria rhizosphaericola JCM 37380 Type strain
"Lacrimispora sanguinis" JCM 37550 Proposed type strain
"Lactiplantibacillus kimchii" JCM 37966 Proposed type strain
"Lactiplantibacillus koreensis" JCM 37965 Proposed type strain
"Marinicella algicola" JCM 35965 Proposed type strain
Marinobacter sp. JCM 15712
Metapseudomonas phytobenefica JCM 37070 Type strain
Methylomonas stagni JCM 36702 Type strain
Microbulbifer discodermiae JCM 37223 Type strain
Mucilaginibacter aureus JCM 37500 Type strain
"Mucilaginibacter florum" JCM 36590 Proposed type strain
"Mucilaginibacter oryzagri" JCM 35894 Proposed type strain
Mucilaginibacter sediminis JCM 37501 Type strain
"Natribacillus halophilus" JCM 15648
"Neobacillus solisequens" JCM 37672 Proposed type strain
"Neobacillus terrisolis" JCM 37671 Proposed type strain
"Neorhizobium lilium" JCM 33731 Proposed type strain
"Ningiella algicola" JCM 35964 Proposed type strain
Paracoccus jiaweipingae JCM 37697 Type strain
Paracoccus zhouxuedongae JCM 37698 Type strain
"Paraniabella aurantiaca" JCM 37728 Proposed type strain
"Pelagithermus desulfuricans" JCM 15748
"Phaeovulum molybdatiresistens" JCM 35387 Proposed type strain
Phenylobacterium glaciei JCM 33227 Type strain
Piscibacillus sp. JCM 15780
Pseudocoprococcus catus JCM 37941 Type strain
Pseudocoprococcus immobilis JCM 37951 Type strain
Pseudodysgonomonas massiliensis JCM 38122 Type strain
Pseudomonas bambusae JCM 36624 Type strain
Pseudomonas tumuqii JCM 34129 Type strain
"Pseudonocardia mahuensis" JCM 34850 Proposed type strain
Ruminococcus sporogenes JCM 36793 Type strain
"Salinisphaera marina" JCM 14955
Sediminibacterium longum JCM 36264 Type strain
"Sphingomonas xanthus" JCM 32376 Proposed type strain
"Spirochaeta pyruvativorans" JCM 15036
Spongorhabdus nitratireducens JCM 37577 Type strain
"Streptomyces dioscori" JCM 32173 Proposed type strain
Streptomyces secundicynarae JCM 37325 Type strain
Thaumasiovibrio clandestinus JCM 37837 Type strain
Thermoanaerovibrio sp. JCM 15583
"Thermodesulfobium fumaratoxidans" JCM 39391 Proposed type strain
Thermorhabdus hydrogeniformans JCM 39573 Type strain
Thermosipho sp. JCM 15584
Undibacter mobilis JCM 32856 Type strain
Unidentified bacterium JCM 15107
Vibrio sabulosilitoris JCM 37826 Type strain
Vibrio sabulosilitoris JCM 37827
Viscerimonas tarda JCM 35195 Type strain
Archaea
"Caldiplasma sukawensis" JCM 39523
"Caldiplasma sukawensis" JCM 39524 Proposed type strain
"Cuniculiplasma thermophilum" JCM 39525
"Cuniculiplasma thermophilum" JCM 39526 Proposed type strain
"Halonovum rutilum" JCM 36641 Proposed type strain
"Halonovum salinarum" JCM 36640 Proposed type strain
Halorubrum sp. JCM 14979
Methanosarcina mangrovi JCM 39553 Type strain
Methanosarcina sediminis JCM 39554 Type strain
Natronoarchaeum sp. JCM 16329
Natronomonas amylolytica JCM 36683 Type strain
"Natronorubrum amylolyticum" JCM 37221 Proposed type strain
"Natronorubrum marinum" JCM 37154 Proposed type strain
"Natronorubrum salinum" JCM 36152 Proposed type strain
Salinarchaeum laminariae JCM 17266
Thermoplasma acidophilum JCM 17944
Thermoplasma acidophilum JCM 17945
Fungi
Bannozyma yamatoana JCM 5975
Bannozyma yamatoana JCM 5976
Bannozyma yamatoana JCM 5977
Bullera alba JCM 6075
Bullera alba JCM 6076
Candida albicans JCM 2302
Candida membranifaciens JCM 2336
Candida metapsilosis JCM 2371
Candida saitoana JCM 2116
Candida saitoana JCM 2117
Candida tropicalis JCM 2301
Candida tropicalis JCM 2303
Candida tropicalis JCM 2377
Candida zeylanoides JCM 2340
Carlosrosaea camelliae JCM 36700 Type strain
Chrysozyma griseoflava JCM 5981
Chrysozyma sp. JCM 5655
Clavispora sp. JCM 2274
Cutaneotrichosporon curvatum JCM 11578
Debaryomyces hansenii JCM 1524
Dioszegia aurantia JCM 36696 Type strain
Dioszegia changbaiensis JCM 5980
Dioszegia foliicola JCM 36695 Type strain
Dioszegia guizhouensis JCM 36694 Type strain
Dioszegia guizhouensis JCM 36697
Farysia photiniae JCM 36715 Type strain
Filobasidium castaneae JCM 35729 Type strain
Filobasidium pseudomali JCM 36693 Type strain
Filobasidium qingyuanense JCM 36688 Type strain
Geotrichum candidum JCM 2452
Geotrichum candidum JCM 2453
Geotrichum klebahnii JCM 2455
Issatchenkia orientalis JCM 3535
Kluyveromyces marxianus JCM 2275
Kockovaella quanzhouensis JCM 36712 Type strain
Kockovaella sambuci JCM 36714 Type strain
Kurtzmaniella quercitrusa JCM 2372
Lipomyces lipofer JCM 5991 Type strain
Magnusiomyces magnusii JCM 6310
Magnusiomyces magnusii JCM 34065
Magnusiomyces magnusii JCM 35273
Magnusiomyces magnusii JCM 35288
Magnusiomyces magnusii JCM 35299
Metschnikowia sp. JCM 2378
Meyerozyma guilliermondii JCM 1540
Monascostroma sphagnophilum JCM 39663
Monascostroma sphagnophilum JCM 39664
Pichia fermentans JCM 2272
Rhodosporidiobolus odoratus JCM 5982
Rhodotorula silvicola JCM 36980 Type strain
Saitozyma ninhbinhensis JCM 16266
Saitozyma ninhbinhensis JCM 16267
Saitozyma podzolica JCM 16268
Saitozyma podzolica JCM 16269
Sporobolomyces japonicus JCM 5737
Vanrija humicola JCM 1529
Vishniacozyma diospyri JCM 36719 Type strain
Vishniacozyma eriobotryae JCM 36716 Type strain
Vishniacozyma guiyangensis JCM 36713 Type strain
Wickerhamomyces guiyangensis JCM 36690 Type strain
Wickerhamomyces paramyanmarensis JCM 36692 Type strain
Wickerhamomyces phyllophilus JCM 36689 Type strain
Wickerhamomyces quanzhouensis JCM 36687 Type strain
Yamadazyma aaseri JCM 2292
Yamadazyma akebiae JCM 36691 Type strain
Yarrowia lipolytica JCM 2346
Yarrowia yakushimensis JCM 12780
Yarrowia yakushimensis JCM 12781
Yarrowia yakushimensis JCM 12783
Zygosaccharomyces bailii JCM 1799
Algae
Coccomyxa sp. JCM 39665
Coccomyxa sp. JCM 39666
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2026.03.19
