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Mucilaginibacter florum sp. nov., isolated from the flower of Coreopsis grandiflora and Mucilaginibacter oryzagri sp. nov., isolated from rice paddy soil in Korea
Parthiban Subramanian, Jun Heo, Daseul Lee, Seunghwan Kim, Hyorim Choi, Yunhee Choi, Yiseul Kim
J. Microbiol. 2025;63(12):e2509014.   Published online December 31, 2025
DOI: https://doi.org/10.71150/jm.2509014
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AbstractAbstract PDFSupplementary Material

Two aerobic, Gram-stain-negative, non-motile and rod-shaped bacterial strains designated GGG-R5T and M4-18T were isolated from flowers of golden wave (Coreopsis grandiflora) and rice paddy soil, respectively in the Republic of Korea. Both strains were pigmented and produced flexirubin-type pigments. Based on phylogenetic analysis using 16S rRNA gene sequence, both strains were placed within the genus Mucilaginibacter with M. agri R11T and M. jinjuensis YC7004T both being the closest relatives to GGG-R5T (97.7%) and in case of M4-18T, M. ginsenosidivorax KHI28T (98.5%) was the nearest neighbor. Characteristic to genus Mucilaginibacter, the major cellular fatty acids in both strains were iso-C15:0, iso-C17:0 3-OH, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c); menaquinone-7 was the major menaquinone and phosphatidylethanolamine was the major polar lipid observed. Comparison of genome sequences with the other members of Mucilaginibacter indicated orthologous average nucleotide identity (orthoANI) at 73.3–73.5% for GGG-R5T and 78.9–88.5% for M4-18T. Digital DNA-DNA hybridization (dDDH) values ranged at 19.1–19.7% between GGG-R5T and its neighbor species. In case of M4-18T, the observed range was at 21.9–36.6%. Considering the 16S rRNA similarity, orthoANI and dDDH values as well as comparison of phenotypic and chemotaxonomic characteristics indicated that both strains belonged to genus Mucilaginibacter but were distinctly distinguishable from previously described species. The strains GGG-R5T and M4-18T, therefore represent distinct novel species for which names Mucilaginibacter florum GGG-R5T and Mucilaginibacter oryzagri M4-18T are proposed. The type strains are GGG-R5T (= KACC 22063T = JCM 36590T) and M4-18T (= KACC 22773T = JCM 35894T).

Journal Article
Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment
Sidra Erum Ishaq, Tariq Ahmad, Lewen Liang, Ruize Xie, Tiantian Yu, Yinzhao Wang, Fengping Wang
J. Microbiol. 2024;62(8):611-625.   Published online July 10, 2024
DOI: https://doi.org/10.1007/s12275-024-00145-w
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AbstractAbstract PDF
Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Citations

Citations to this article as recorded by  
  • Engineering the phycosphere: fundamental concepts and tools for the bottom-up design of microalgal-bacterial consortia
    Austin Semple, Jagroop Pandhal
    Applied Phycology.2025; 6(1): 21.     CrossRef
  • Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea
    Abhay B. Fulke, Nilkanth Sharma, Jayshree Nadekar
    Microbial Ecology.2025;[Epub]     CrossRef
  • The bacterial community of the freshwater bryozoan Cristatella mucedo and its secondary metabolites production potential
    Inmaculada Tocino-Márquez, Martin Zehl, Joana Séneca, Petra Pjevac, Manuel Felkl, Christian F. W. Becker, Alexander Loy, Thomas Rattei, Andrew N. Ostrovsky, Sergey B. Zotchev
    Scientific Reports.2025;[Epub]     CrossRef
  • Uncertainty Analysis of Biogas Generation and Gas Hydrate Accumulations in the Baiyun Sag, South China Sea
    Pibo Su, Jinqiang Liang, Huai Cheng, Yaoyao Lv, Wei Zhang, Zuofei Zhu
    Microorganisms.2024; 13(1): 5.     CrossRef

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