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RIKEN BioResource Research Center - Japan Collection of Microorganisms
JCM Mail News (2026.06.11)
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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: Reclassification of the Genus Dysgonomonas and
Description of Novel Species
- Revision of Distribution Fees for Bioresources in RIKEN BRC
- List of 'Yeast strains with specific characteristics' updated
- Newly cataloged strains (2026.04.01 - 2026.05.31)
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- Special topic: Reclassification of the Genus Dysgonomonas and
Description of Novel Species
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The genus Dysgonomonas belongs to the family Dysgonomonadaceae within
the order Bacteroidales. It comprises facultatively anaerobic,
fermentative bacteria that have been isolated from a wide range of
environments, including human clinical specimens, sea sand, the human
gut and termite hindguts. Some members of this genus have been
isolated from immunocompromised patients and are therefore regarded as
opportunistic pathogens. At the same time, Dysgonomonas species and
related bacteria have also been frequently detected in the guts of
insects such as termites and cockroaches. Because their genomes encode
numerous carbohydrate-active enzymes, they may contribute to the
degradation of plant-derived materials consumed by their host insects.
In recent years, not only cultivated isolates of Dysgonomonas from
insect guts but also 16S rRNA gene sequences of uncultured bacteria
closely related to Dysgonomonas have been increasingly reported. These
findings have drawn attention to the diversity of this bacterial group.
However, since the genus Dysgonomonas was proposed in 2000, no
comprehensive taxonomic revision of the genus has been conducted, and
the criteria defining the genus have remained unclear.
In this study, we re-examined the taxonomy of the genus Dysgonomonas
based on both genomic information and physiological characteristics
(Takahashi et al., 2026).
First, we compared the whole genomes of previously reported
Dysgonomonas species and two strains newly isolated from the gut of a
termite. Specifically, we examined how similar the shared proteins
were between bacterial genomes, using average amino acid identity,
and how many proteins were shared between them, using the percentage
of conserved proteins. These analyses revealed that the bacteria
previously assigned to the genus Dysgonomonas formed several groups
with high genomic similarity within each group, separated by clear
gaps between groups. These groups also corresponded well to the
phylogenetic relationships inferred from genome sequences.
We further compared available physiological data and found that indole
production differed among Dysgonomonas species. This difference
largely corresponded to the groups identified by genome-based
comparisons.
Based on these results, we concluded that the previously recognized
genus Dysgonomonas would be more appropriately divided into multiple
genera rather than treated as a single genus. In this study, we
proposed the genus Dysgonomonas sensu stricto, including Dysgonomonas
gadei; the new genus Indolivaga, represented by Dysgonomonas
capnocytophagoides; and the new genus Pseudodysgonomonas, represented
by Dysgonomonas massiliensis. In addition, among the two strains newly
isolated from the termite gut, one was assigned to a novel species
within Dysgonomonas sensu stricto, whereas the other was considered to
represent a novel species belonging to a new genus distinct from the
existing Dysgonomonas lineage. For the latter, we proposed the new
genus Viscerimonas.
This reclassification provides a taxonomic framework for organizing
the diversity of Dysgonomonas-related bacteria that are frequently
found in insect guts. It will also provide an important basis for
future studies on the ecological roles of these bacteria in the insect
gut environment.
The newly isolated microorganisms and the names proposed in this
taxonomic revision are introduced below.
- JCM 35194 Dysgonomonas reticulitermitis
This strain was isolated from the gut of the subterranean termite
Reticulitermes speratus, which is widely distributed in Japan. It
produces indole. The specific epithet reticulitermitis is derived from
Reticulitermes, the genus name of the termite from which the strain
was isolated.
- JCM 35195 Viscerimonas tarda
This strain was isolated from the gut of the subterranean termite
Reticulitermes speratus. It does not produce indole. The genus name
Viscerimonas means "a monad inhabiting the intestines." The specific
epithet tarda means "slow" or "inactive" in Latin and refers to
the slow growth of this strain.
- Indolivaga
The genus name Indolivaga is derived from indolum, meaning indole,
and vagus, meaning wandering, roaming or unfixed. The name implies
"an organism wandering away from indole," referring to the lack of
involvement in indole production. This genus includes species
previously classified as Dysgonomonas capnocytophagoides,
Dysgonomonas macrotermitis and Dysgonomonas alginatilytica.
- Pseudodysgonomonas
The genus name Pseudodysgonomonas is derived from pseudo-, meaning
false, and Dysgonomonas. It means "a false Dysgonomonas," indicating
an organism that resembles Dysgonomonas but does not belong to
Dysgonomonas sensu stricto. This genus includes the species previously
classified as Dysgonomonas massiliensis.
Reference
Takahashi K, Hisatomi A, Mori K, et al. Reclassification of the genus
Dysgonomonas and description of Dysgonomonas reticulitermitis sp. nov.
and Viscerimonas tarda gen. nov., sp. nov. from the gut of the
subterranean termite Reticulitermes speratus.
Int J Syst Evol Microbiol. 2026;76(1):007031.
doi:10.1099/ijsem.0.007031
Kazuki Takahashi Ph.D.
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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://jcm.brc.riken.jp/en/fee2026_en
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List of 'Yeast strains with specific characteristics' updated
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We have updated the list of 'Yeast strains with specific characteristics'.
The database now contains 2,431 entries, up from 1,415, and you can
now sort the strains that have ability to ferment glucose and fructose,
as well as by growth at 40°C and 42°C. Please take advantage of this
enhanced yeast resource search for your research.
Yeast strains with specific characteristics.
https://www.jcm.riken.jp/cgi-bin/jcm/function?KEY=YEAST
Rikiya Endoh (curator of yeasts and yeast-like algae)
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- Newly cataloged strains (2026.04.01 - 2026.05.31)
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Bacteria
"Acinetobacter kanungonis subsp. JCM 36322 Proposed type strain
fragariae"
"Acinetobacter minutum" JCM 36321 Proposed type strain
Affinundibacterium flavidum JCM 34286 Type strain
Alteriqipengyuania triglochinis JCM 36262 Type strain
Arthrobacter antibioticus JCM 36082 Type strain
Arthrobacter endolithicus JCM 36079 Type strain
"Arthrobacter rhizophilus" JCM 35693 Proposed type strain
Daquilactobacillus linshuiensis JCM 38144 Type strain
"Denitratimonas organivorans" JCM 36229 Proposed type strain
Desulforhopalus glucosivorans JCM 39400 Type strain
"Desulforudis audaxviator" JCM 39285 Proposed type strain
"Desulfosceptrum tomskiensis" JCM 39286 Proposed type strain
"Desulfosporosinus shakirovi" JCM 39189 Proposed type strain
Desulfosporosinus sp. JCM 32883
Dokdonella aquatica JCM 36943 Type strain
"Dyella stictolepturae" JCM 37315 Proposed type strain
Enterococcus salsurae JCM 37829 Type strain
"Kamagatella elastica" JCM 39611 Proposed type strain
Magnetococcus organivorans JCM 39466 Type strain
Magnetovibrio massiliensis JCM 39465 Type strain
"Maridesulfovibrio caeruleilacunae" JCM 39061 Proposed type strain
"Maridesulfovibrio oucae" JCM 39062 Proposed type strain
"Microbacterium bengalense" JCM 37885 Proposed type strain
"Microbacterium fluminis" JCM 38050 Proposed type strain
Microbacterium hanjuni JCM 37689 Type strain
Microbacterium shimangi JCM 37690 Type strain
Microbacterium songi JCM 37688 Type strain
Microbacterium triticisoli JCM 35796 Type strain
Micromonospora yongxingensis JCM 38260 Type strain
Mycolicibacterium chengduense JCM 37531 Type strain
Mycolicibacterium sichuanense JCM 37529 Type strain
"Niallia laureatilytica" JCM 36811 Proposed type strain
Paeniglutamicibacter selenitireducens JCM 37299 Type strain
"Paramicrobacterium salitolerans" JCM 36217 Proposed type strain
Parvimonas oralis JCM 37774 Type strain
Parvimonas pharyngis JCM 37775 Type strain
Paucilactobacillus salsurae JCM 37828 Type strain
"Pseudochrobactrum albidum" JCM 37008 Proposed type strain
Qipengyuania triglochinis JCM 36263 Type strain
Rhodococcus huquni JCM 34841 Type strain
Rhodococcus mengyinensis JCM 36291 Type strain
Rhodococcus quanlei JCM 34842 Type strain
Rhodococcus ruitaii JCM 34787 Type strain
Rhodococcus shunpengi JCM 36290 Type strain
Ruegeria hyattellae JCM 37352 Type strain
Ruegeria jejuensis JCM 37225 Type strain
"Saccharothrix camelliae" JCM 37292 Proposed type strain
Sphingomonas benefaciens JCM 37846 Type strain
Sphingomonas cellulosilytica JCM 37845 Type strain
Sphingopyxis selenitireducens JCM 37246 Type strain
Stenotrophomonas tuberculopleuritidis JCM 36489 Type strain
Streptococcus bovismuti JCM 37064 Type strain
Streptomyces dryopteridis JCM 38134 Type strain
"Streptomyces kryoterrae" JCM 37994 Proposed type strain
"Streptomyces ruilongensis" JCM 35794 Proposed type strain
"Streptomyces yamdrokensis" JCM 37995 Proposed type strain
Tateyamaria algicola JCM 36649 Type strain
Tateyamaria rhodophyticola JCM 35962 Type strain
Terasakiella magnetica JCM 39464 Type strain
Archaea
"Haloarchaeobius caseinilyticus" JCM 37971 Proposed type strain
"Haloarchaeobius pelagicus" JCM 37972 Proposed type strain
Methanobacterium sp. JCM 18473
Fungi
Tschermakia inclusa JCM 39667 ex-paratype strain
Tschermakia inclusa JCM 39668 ex-holotype strain
Algae
Radiococcus sp. JCM 39669
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Microbe Division / Japan Collection of Microorganisms
RIKEN BioResource Research Center
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2026.06.11
