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Phocaeicola acetigenes sp. nov., producing acetic acid and iso-butyric acid, isolated faeces from a healthy human

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Abstract

An obligately anaerobic, non-motile, Gram-stain-negative, and rod-shaped strain KGMB11183T was isolated from the feces of healthy Koreans. The growth of strain KGMB11183T occurred at 30–45 °C (optimum 37 °C), at pH 6–9 (optimum pH 7), and in the presence of 0–0.5% NaCl (optimum 0%). Strain KGMB11183T showed 16S rRNA gene sequence similarities of 95.4% and 94.2% to the closest recognized species, Phocaeicola plebeius M12T, and Phocaeicola faecicola AGMB03916T. Phylogenetic analysis showed that strain KGMB11183T is a member of the genus Phocaeiocla. The major end products of fermentation are acetic acid and isobutyric acid. The major cellular fatty acids (> 10%) of this isolate were C18:1 cis 9, anteiso-C15:0, and summed feature 11 (iso-C17:0 3-OH and/or C18:2 DMA). The assembled draft genome sequences of strain KGMB11183T consisted of 3,215,271 bp with a DNA G + C content of 41.4%. According to genomic analysis, strain KGMB11183T has a number of genes that produce acetic acid. The genome of strain KGMB11183T encoded the starch utilization system (Sus) operon, SusCDEF suggesting that strain uses many complex polysaccharides that cannot be digested by humans. Based on the physiological, chemotaxonomic, phenotypic, and phylogenetic data, strain KGMB11183T is regarded a novel species of the genus Phocaeicola. The type strain is KGMB11183T (= KCTC 25284T = JCM 35696T).

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Data availability

The sequences of 16S rRNA gene and genome of strain KGMB11183T have been deposited in GenBank/EMBL/DDBJ with the accession numbers OQ101910 and JAPZVM000000000, respectively. Three supplementary figures are available with the online version of this article.

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Acknowledgements

We thank Professor Bernhard Schink and Aharon Oren for his advice in naming the novel strain.

Funding

This work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT) of the Republic of Korea (NRF- 2016M39A9F3947962) and a grant from the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research initiative program (KGM5232323).

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Authors and Affiliations

  1. Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea

    Hyo Eun Do, Young Bong Ha, Ji-Sun Kim, Min Kuk Suh, Han Sol Kim, Mi Kyung Eom, Ju Huck Lee, Seung-Hwan Park, Se Won Kang & Jung-Sook Lee

  2. Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea

    Hyo Eun Do

  3. Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea

    Min Kuk Suh & Han Sol Kim

  4. Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-Gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea

    Dong Ho Lee & Hyuk Yoon

  5. CJ Bioscience, Inc., 14 Sejong-Daero, Jung-gu, Seoul, 04527, Republic of Korea

    Je Hee Lee

  6. University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea

    Jung-Sook Lee

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Contributions

Isolation of gut bacteria and taxonomy analysis were performed by HED, YBH, JSK, HSK, MKS, MKE, JHL, SHP, and SWK. Whole-genome analysis was performed by JHL. The first draft of the manuscript was written by HED. All authors read and approved the final manuscript. Conceptualization: JSL. Formal analysis and investigation: HED. Writing—original draft preparation: HED. Writing—review and editing: JSK and JSL. Funding acquisition: JSL. Resources: JSK, MKS, MKE, JHL, SHP, SWK, DHL, HY, and JHL. Supervision: JSL.

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Correspondence to Jung-Sook Lee.

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This study was conducted in accordance with the IRB regulation at KCTC (P01-201702-31-007).

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Do, H.E., Ha, Y.B., Kim, JS. et al. Phocaeicola acetigenes sp. nov., producing acetic acid and iso-butyric acid, isolated faeces from a healthy human. Antonie van Leeuwenhoek 117, 30 (2024). https://doi.org/10.1007/s10482-024-01930-8

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