- Volume 75, Issue 2, 2025

In this article, it is proposed that the Nichols strain of Treponema pallidum be established as the type strain. T. pallidum was first identified as the causative agent of syphilis in 1905, and the Nichols strain was isolated in 1912 by inoculation of a rabbit with cerebrospinal fluid from a patient with neurosyphilis. The Nichols strain has been maintained by serial passage in rabbits for over a century, and historically most studies of T. pallidum have been conducted using this strain. In recent years, a procedure for continuous in vitro culture of T. pallidum in a tissue culture system has been developed, making propagation of this spirochaete easier and hence facilitating research. The Nichols strain has >99% DNA homology with a group of organisms that cause syphilis, bejel/endemic syphilis and yaws in humans, a yaws-like disease in primates and spirochaetosis in rabbits and hares. This group is highly similar in terms of their gene and G+C content, genome synteny, cell morphology, natural dependence on mammalian hosts and ability to cause long-term infections; variation occurs in host range, modes of transmission, aptitude for dissemination, manifestations, congenital infection and geographical distribution. Availability of a type strain will aid in the formal acceptance of T. pallidum subspecies first described in 1984 and supported by recent whole-genome analyses of numerous strains from the T. pallidum-related group.

A Gram-stain-positive, aerobic and non-motile actinobacterium, designated strain MR15.9T, was isolated from sediment collected from a mangrove ecosystem in Semarang city, Indonesia. Strain MR15.9T grew at 4–37 °C (optimum 30 °C), pH 6.0–11.0 (optimum 7.0–8.0), with 0–10% (w/v) NaCl (optimum 0–3%). The genome of strain MR15.9T was 3.67 Mbp with 71.7 mol% G+C content. Phylogenetic analysis based on 16S rRNA gene sequence and genome sequence directed that strain MR15.9T formed a well-supported clade with Tersicoccus solisilvae CGMCC 1.15480T and Tersicoccus phoenicis 1P05MAT and shared the highest similarity to T. solisilvae CGMCC 1.15480T (98.9% sequence similarity) and T. phoenicis 1P05MAT (98.6% sequence similarity). However, the comparative genome analysis between strain MR15.9T and T. solisilvae CGMCC 1.15480T gave average nt identity value of 85.2% and digital DNA–DNA hybridization value of 29.0%, which were below the statistical threshold for the delineation of the species. Chemotaxonomic data showed that the major fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. MK-8(H2) and MK-9(H2) were noted as the predominant respiratory quinones in this strain. The results of polyphasic characterization indicated that strain MR15.9T represents a novel species of the genus Tersicoccus. The name Tersicoccus mangrovi sp. nov. is proposed, with the type strain MR15.9T (=MCCC 1K08875T=KCTC 59105T).

Three strains, designated as J27, J71T and J72, belonging to the genus Antrihabitans, were isolated from stable foams formed in activated sludge wastewater treatment plants (WWTPs) in New South Wales, Australia. Phenotypic and genomic analyses revealed that these strains belong to the Nocardiaceae family and are closely related to Antrihabitans stalagmiti. However, distinct genomic and physiological characteristics, including overall genomic relatedness indices, phylogenomic analysis, genomic metabolic profiles and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry), confirmed their status as a new species.

Ecologically, these strains showed a wide metabolic versatility, like enhanced membrane transport systems for amino acids, metals and phosphate, as well as the ability to synthesize mycolic acids, contributing to their hydrophobic nature and involvement in foam stabilization. Their adaptations likely provide a competitive advantage in WWTPs, where they persist in nutrient-rich, metal-laden and foam-stabilizing environments. The species did not present the typical rod-coccus cycle, described previously as a defining characteristic of the Antrihabitans genus. Based on their unique genomic, phenotypic and ecological features, we propose the name Antrihabitans spumae sp. nov., with strain J71T (JCM 34493T, NCIMB 15450T) designated as the type strain. Additional strains include J27 (JCM 33914, NCIMB 15449) and J72 (NCIMB 15448).

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-01T, was isolated from the sediment sample of the piston core collected at station 3 at Good Weather Ridge area offshore southwestern Taiwan from ORI-902A cruise in 2009. Cells of strain CWC-01T are rod-shaped, measuring 0.4–0.5 µm in width and 1.0–2.0 µm in length. Strain CWC-01T utilizes formate and H2/CO2 to produce methane, but not secondary alcohol, methanol, ethanol, methylamines or acetate as catabolic substrates. The optimal growth conditions are 37 °C, 0.043 M NaCl and pH 6.3. Growth effectors tests indicate tryptone, but not acetate and yeast extract, could stimulate the growth of strain CWC-01. Phylogenetic analysis of 16S rRNA gene reveals that strain CWC-01T is most closely related to Methanobacterium petrolearium Mic5c12T, with 96.63% identity. Genome size of strain CWC-01T is 1.98 Mb and it is the smallest genome size of genus. The genomic DNA G+C content obtained from the genome sequence of strain CWC-01T is 44.15 mol%. Based on these phenotypic, phylogenetic and genomic analyses, we propose that strain CWC-01T represents a novel species in genus Methanobacterium, for which the name Methanobacterium aridiramus sp. nov. is proposed. The type strain is CWC-01T (=BCRC AR10053T=NBRC 113991T).

Two Gram-stain-negative, facultative anaerobic, rod-shaped and non-gliding bacteria, designated as HL-DH10T and HL-DH14, were isolated from the halophyte Suaeda japonica in a mudflat, Republic of Korea. Based on the results of 16S rRNA gene pairwise analysis, the two isolates were the members of the family Flavobacteriaceae, and Aestuariibaculum suncheonense SC17T was the most closely related to strains HL-DH10T and HL-DH14 with 96.3% and 95.4% sequence similarity, respectively. The average nt identity and digital DNA–DNA hybridization values between strains HL-DH10T and HL-DH14 and other related species were all less than 79.2% and 21.9%, respectively. The genomic DNA G+C contents of strains HL-DH10T and HL-DH14 were 32.0% and 31.5%, respectively. Cells of these strains showed optimal growth at 25 °C, pH 6.5–7.0 and 2.5–4.0% (w/v) sea salts. The major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C15:0 (14.0–16.0%), iso-C15:1 G (10.0–12.0%), iso-C17:0 3-OH (12.4–13.9%), iso-C15:0 3-OH (11.8–14.9%) and anteiso-C15:0 (9.4–10.6%). The polar lipids consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two to three unidentified aminolipids and three unidentified lipids. The comprehensive phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strains HL-DH10T and HL-DH14 are considered to represent a novel genus of Flavobacteriaceae. Hence, we propose the novel genus Thalassobellus suaedae gen. nov., sp. nov. The type strain is HL-DH10T (=KCCM 90512T=JCM 36598T).

A novel yellow-coloured bacterial strain MA10T was isolated from mangrove sediment and subjected to polyphasic taxonomic identification. Strain MA10T was Gram-negative, rod-shaped, catalase-positive and oxidase-positive. Carotenoid pigment was present, and flexirubin-type pigment was absent. The 16S rRNA gene of strain MA10T had the highest sequence similarity with Tamlana crocina HST1-43T of 94.5%. The genome size was 3.77 Mbp with a genomic G+C content of 36.3%. The phylogenetic analysis of the 16S rRNA gene sequence and whole-genome sequence showed that strain MA10T belonged to the genus Tamlana of the family Flavobacteriaceae and tightly clustered with T. crocina HST1-43T. The digital DNA–DNA hybridization value and average nucleotide identity value between strain MA10T and T. crocina HST1-43T were 20.4 and 76.7%, respectively. The major menaquinone was MK-6. The major fatty acids (>10 %) were iso-C15:0 (41.6%) and iso-C15:1 G (16.8%). The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. Based on the present polyphasic taxonomic study, strain MA10T was considered to represent a novel species of the genus Tamlana, for which the name Tamlana flava sp. nov. was proposed. The type strain was MA10T (=MCCC 1K09289T=KCTC 102321T). Additionally, the phylogeny of the 16S rRNA gene and whole-genome sequences found that the hitherto described nine species of the genus Tamlana and Algibacter onchidii presented polyphyletic clades, which could be divided into five different genera. The average amino acid identity value of 80% was chosen as the boundary of the five genera. Thus, except for the genus Tamlana, four novel genera named Allotamlana gen. nov., Cognatitamlana gen. nov., Neotamlana gen. nov. and Pseudotamlana gen. nov. were proposed. This study provided valuable taxonomic analysis of the genus Tamlana.

Three novel strains, designated LB3P45T, LS2P90T and ZS1P70T, were isolated from glaciers located on the Tibetan Plateau, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and yellow or orange coloured. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they belong to the genus Flavobacterium. The 16S rRNA gene sequence similarity among the three strains ranged from 97.4 to 98.6%. Strain LB3P45T showed 98.9% and 98.7% similarity to Flavobacterium urumqiense CGMCC 1.9230T and Flavobacterium xinjiangense JCM 11314T, respectively. Strain LS2P90T displayed 99.0% and 98.7% similarity to F. xinjiangense JCM 11314T and F. urumqiense CGMCC 1.9230T. Strain ZS1P70T had the highest sequence similarity with F. xinjiangense JCM 11314T (98.0%) and F. urumqiense CGMCC 1.9230T (97.8%). The average nucleotide identity and digital DNA–DNA hybridization values between these strains and their closest relatives were lower than 93.0% and 47.9%, respectively. All three strains contained summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as the major fatty acids. Based on phenotypic characteristics, phylogenetic analysis and genotypic data, the three novel species are proposed: Flavobacterium fructosi sp. nov. (LB3P45T=CGMCC 1.11439T=NBRC 114819T), Flavobacterium xylosi sp. nov. (LS2P90T=CGMCC 1.11685T=NBRC 114823T) and Flavobacterium zhouii sp. nov. (ZS1P70T=CGMCC 1.24124T=NBRC 114829T).

Three novel coccoid-shaped strains, designated 21WXBC0057M1T, 21WXBC0044M1T and BJSWXB5TM5T, were isolated from human breast milk in Wuxi, Jiangsu Province, China. These strains were facultative anaerobes, catalase-negative and Gram-positive. Through a comprehensive analysis of rRNA genes, protein-coding housekeeping genes and genomic phylogeny, we identified these strains as belonging to the genus Streptococcus. Specifically, strain 21WXBC0057M1T was phylogenetically most closely related to Streptococcus infantis, strain 21WXBC0044M1T was most closely related to Streptococcus oralis and strain BJSWXB5TM5T displayed similarities to Streptococcus australis, Streptococcus peroris and S. infantis. The pairwise average nucleotide identity and digital DNA–DNA hybridization values for these three strains were below 95 and 70%, respectively, indicating that they occupied evolutionary branches distinct from all previously validly published Streptococcus species. Distinctive phenotypic characteristics discriminated these novel species from the type strains of their most closely related species. The major cellular fatty acids in the three strains were C16 : 0 and C18 : 0. Genome annotation and a thorough examination of carbohydrate-active enzyme distribution highlighted the observation that all strains possessed extensive capabilities for carbohydrate metabolism, particularly human milk oligosaccharides utilization. Thus, based on these findings, we proposed the classification of the strains as representing three novel species within the genus Streptococcus: Streptococcus wuxiensis sp. nov. (type strain 21WXBC0057M1T=GDMCC 1.4126T=KCTC 25760T), Streptococcus jiangnanensis sp. nov. (type strain 21WXBC0044M1T= GDMCC 1.4127T=KCTC 25762T) and Streptococcus fermentans sp. nov. (type strain BJSWXB5TM5T=GDMCC 1.4130T=KCTC 25759T).

Strain JR3T was isolated from Chinese pickled potherb mustard (Brassica juncea Coss.) purchased from a local market in Shanghai, China. A polyphasic approach including 16S rRNA gene sequence analysis, average nucleotide identity (ANI) analysis, digital DNA–DNA hybridization (dDDH), determination of G+C content and various phenotypic analyses was employed to characterize strain JR3T. The bacterium was rod-shaped, Gram-stain-positive, terminal round endospore-forming and catalase-positive. The strain could grow at a wide range of temperatures (20–45 °C) and pH values (6.0–8.0). Optimal growth of strain JR3T occurred at 35–40 °C and a pH value of 7.0. The strain exhibited growth at salt (NaCl) concentrations of up to 3% (w/v). The G+C content of the genomic DNA was 44.0 mol%. The major fatty acids were C16 : 0, C19 : 0 c9, 10, summed feature 10 (C18 : 1 c11/t9/t6) and C18 : 1 c9. 16S rRNA gene sequencing revealed that strain JR3T represents a member of the genus Lacrimispora, and it has higher sequence similarity with Lacrimispora amygdalina BR-10T (=DSM 12857T) (98.72%), Lacrimispora saccharolyticum WM1T (98.29%) and Lacrimispora xylanolytica sy1 (98.22%). The dDDH value for strain JR3T and phylogenetically related species within the genus Lacrimispora ranged from 17.7% to 29.9%. The ANI of strain JR3T with its closely related taxa was far lower than the threshold (95%−96%) used for species differentiation. Results of phylogenetic, physiological and phenotypic characterization confirmed that strain JR3T represented a novel species within the genus Lacrimispora, for which the name Lacrimispora sinapis sp. nov. is proposed. The type strain is JR3T=CCTCC AB 2024044T=LMG 33655T.

In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864T (JF-1T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108T (=JCM 39522T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.

Phytopathogenic bacteria (MAFF 311311T and MAFF 311313) were isolated from sugarcane plants exhibiting leaf stripe symptoms associated with red stripe disease in Okinawa Prefecture, Japan. The strains were Gram-reaction-negative, aerobic, motile with one polar flagellum, rod-shaped and non-spore-forming. The genomic DNA G+C content was 69.0 mol%, and the major cellular fatty acids (>10 % of the total fatty acids) included summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). Phylogenomic analyses using whole-genome sequences consistently placed these strains within the genus Acidovorax. However, their phylogenetic positions did not correspond to any known species within this genus. Comparative analyses, including average nucleotide identity and digital DNA–DNA hybridization with closely related species, yielded values below the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively), with the highest values observed for Acidovorax oryzae ATCC 19882T (93.98 and 54.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and a repertoire of secretion systems and their effectors can differentiate these strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study indicate that MAFF 311311T and MAFF 311313 constitute a novel species within the genus Acidovorax, for which we propose the name Acidovorax sacchari sp. nov., with MAFF 311311T (=ICMP 25276T) designated as the type strain.

Two motile bacterial strains, designated as cfHf56-1T and SW 252, were isolated from the coelomic fluid of Holothuria forskali and from the surrounding seawater at the animal sampling site, respectively. The sea cucumber was collected in the Glénan archipelago (Brittany, France). Strains cfHf56-1T and SW 252 were Gram-stain-negative, non-spore-forming and rod-shaped bacteria. Colonies made on marine agar plates were brown in color. The pH and temperature ranges for growth were 7–8 and 18–30 °C, respectively, in marine broth. The major fatty acids were 16 : 1 cis9 and 16 : 0. Phylogenetic analyses evidenced that both strains belong to a novel species in the genus Pseudoalteromonas. The strains were closely related to the type strains of Pseudoalteromonas caenipelagi, Pseudoalteromonas byunsanensis and Pseudoalteromonas amylolytica, with 75–78 % ANI and 19–21 % dDDH values. In this context, cfHf56-1T (= CIP 111854T = CECT 30642T) is considered as the type strain of the novel species for which the name Pseudoalteromonas holothuriae sp. nov. is proposed. The genome of the type strain is characterized by a size of 5.1 Mbp and a G+C content of 40.5%.

Twenty-nine hippuricase-positive Campylobacter strains were isolated from wild birds and river water. Previous characterization using atpA typing indicated that these strains were related to Campylobacter jejuni and Campylobacter coli but were most similar to three recently described hippuricase-positive Campylobacter species recovered from zebra finches, i.e. C. aviculae, C. estrildidarum and C. taeniopygiae. Phylogenetic analyses using 330 core genes placed the 29 strains into a clade well separated from the other Campylobacter taxa, indicating that these strains represent a novel Campylobacter species. Pairwise digital DNA–DNA hybridization and average nucleotide identity values were below 70 and 95 %, respectively, thus providing further supporting evidence of a novel taxon. Standard phenotypic testing was performed. All strains are microaerobic or anaerobic, motile, Gram-negative, spiral cells that are oxidase, catalase and nitrate reductase positive, but urease negative. Genomic analyses indicate that the 29 strains can potentially synthesize very few amino acids de novo and are auxotrophic for many amino acids and cofactors, similar to the species composing the Campylobacter lari group. In addition, these strains encode complete Entner–Doudoroff and Leloir pathways, suggesting that they may possess the ability to utilize both glucose and galactose; these pathways were also identified in the genomes of the zebra finch-associated taxa. The data presented here show that these strains represent a novel species within Campylobacter, for which the name Campylobacter molothri sp. nov. (type strain RM10537T=LMG 32306T=CCUG 75331T) is proposed.

Bacterial strains, designated DD3T and DDX28, were isolated from field soil in Japan. The strains had the ability to use 2,4-dichlorophenoxyacetic acid as the sole carbon source. They were Gram-reaction-negative, oxidase-positive, weakly catalase-positive, aerobic and non-spore-forming. Their cells were rod-shaped and often lacked flagella, but some exhibited motility due to the presence of one or two polar flagella. The genomic DNA G+C content was 58.8 mol%, and the major cellular fatty acids (>10% of the total fatty acids) were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C18 : 0 and C17 : 0 cyclo. Phylogenetic analyses based on gyrB gene sequences and phylogenomic analysis using whole-genome sequences confirmed that the strains belong to the genus Afipia; however, their phylogenetic position did not match that of any known species of this genus. Comparative studies of the average nucleotide identity and digital DNA–DNA hybridization with closely related species revealed values lower than the thresholds used for prokaryotic species delineation (95–96 and 70%, respectively), with the highest values observed for Afipia broomeae ATCC 49717T (79.92 and 21.5%, respectively). Phenotypic characteristics, cellular fatty acid composition and specific metabolic processes and biosynthetic gene clusters could differentiate the strains from their closest relatives. Our phenotypic, chemotaxonomic and genotypic data indicate that DD3T/DDX28 constitute a novel Afipia species, for which we propose the name Afipia dichlorophenoxyacetatis sp. nov., with DD3T (MAFF 311804T=ICMP 25015T) as the type strain.

The poles of the Earth harbour many novel micro-organisms that have not yet been isolated and identified. Here, a Gram-stain-negative, motile, aerobic and rod-shaped bacterial strain, designated as wDCs-4T, was isolated from surface seawater collected from the Weddell Sea in Antarctica. It grows at 4–40 °C (optimum 10–15 °C), pH 4–8 (optimum 7) and in the presence of 0–4% NaCl (w/v, optimum 0.5–1%). The complete 16S rRNA gene of strain wDCs-4T had maximum sequence identity with Oceanobacter mangrovi SM2-42T (97.2%), followed by Thalassolituus oleivorans MIL-1T (96.5%) and Oceanobacter kriegii 197T (96.2%). Phylogenetic analyses based on the 16S rRNA gene and genome sequences showed that strain wDCs-4T was closely clustered with the members of the genus Oceanobacter and formed an independent clade, which could be considered a monophyletic taxon. The average nucleotide identity values between strain wDCs-4T and the members of the genera Oceanobacter and Thalassolituus were 77.7–78.1 and 77.4–80.5%, respectively. The corresponding digital DNA‒DNA hybridization values are 19.5–20.1 and 20.5–22.4%, respectively. The major fatty acids (>5%) of strain wDCs-4T comprised summed feature 5 (C18:0 ante/C18:2  ω6,9c or C18:2  ω6,9c/C18:0 ante) and C16:0. The predominant respiratory was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, aminolipids and unknown polar lipids. The draft genome size was 4.58 Mbp, with a DNA G+C content of 53.4 mol%. On the basis of polyphasic analyses, strain wDCs-4T represented a novel species in the genus Oceanobacter, for which the name Oceanobacter antarcticus sp. nov. was proposed. The type strain was wDCs-4T (=MCCC 1A20726T=KCTC 8314T).

Strains P94T, B95T and R96T were isolated from apparently healthy fragments of the coral Montipora capitata, which were resistant to Vibrio coralliilyticus infection, from the reef surrounding Moku o Loʻe in Kāne‘ohe Bay, O‘ahu, Hawai‘i, USA, and were taxonomically evaluated using a polyphasic approach. Phylogenetic and phylogenomic analyses placed strains P94T, B95T and R96T within the Pseudoalteromonas genus and most closely related to Pseudoalteromonas luteoviolacea and Pseudoalteromonas rubra. Following genome sequencing of strains P94T, B95T and R96T, the average nt identity and in silico DNA–DNA hybridization comparisons with closely related strains resulted in values that fell below species-level cutoffs. Based on a polyphasic characterization and differences in genomic and taxonomic data, strains P94T, B95T and R96T represent novel species, for which the names Pseudoalteromonas ardens sp. nov., Pseudoalteromonas obscura sp. nov. and Pseudoalteromonas umbrosa sp. nov. are proposed. The type strains are R96T (=DSM 114998T=LMG 32870T), P94T (=DSM 114996T=LMG 32871T) and B95T (=DSM 114997T=LMG 32872T), respectively.

A Gram-negative, rod-shaped and light pink-pigmented bacterial strain, designated Amp-Y-6T, was isolated from the culture of a dinoflagellate Amphidinium carterae CCMP1314. It can produce bacteriochlorophyll a. The 16S rRNA gene of strain Amp-Y-6T had the highest sequence similarity with Roseicyclus marinus CCMM001T of 98.1%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Amp-Y-6T was affiliated to the genus Roseicyclus and formed a monophyletic clade with R. marinus CCMM001T and Roseicyclus mahoneyensis ML6T. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity between strain Amp-Y-6T and the two phylogenetic relatives were 22.7–22.8, 80.4–80.5 and 79.5–80.2%, respectively. The respiratory quinone was Q-10. The major fatty acid composition was summed feature 8 (C18:1  ω7c and/or C18:1  ω6c). The draft genome size was 3.8 Mbp with a genomic G+C content of 68.1 mol%. Gene annotation showed that Amp-Y-6T contained a gene cluster responsible for the C-P degradation, indicating that it had the potential to provide a phosphate source for the dinoflagellate. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain Amp-Y-6T represents a novel species, for which the name Roseicyclus amphidinii sp. nov. is proposed. The type strain is Amp-Y-6T (=MCCC 1K08249T=KCTC 92882T).