Saccharibacteria (Formerly TM7) and Patescibacteria
In 2015, our team has cultivated the first-ever member of all the Candidate Phyla Radiation or Patescibacteria Phlyum (GTDB taxonomy). Nanosynbacter lyticus strain TM7x
He, Xuesong#, McLean, Jeffrey S.#*(co-first author, co-corresponding author), Edlund, Anna, Yooseph, Shibu, Hall, Adam P., Liu, Su-Yang, Dorrestein, Pieter C., Esquenazi, Eduardo, Hunter, Ryan C., Cheng, Genhong, Nelson, Karen E., Lux, Renate, Shi, Wenyuan. (2015) Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences 112(1):244-249.
The publications below highlight the progress in characterization of these novel ultrasmall parasitic epibionts across the human microbiome, mammalian and environment.
Candidate Phlya Radiation
Candidatus Saccharibacteria
GTDB taxonomy: Patescibacteria Phlyum
GTDB taxonomy: Class Saccharimonadia
2023
Wang, Y., Gallagher, L.A., Andrade, P.A., Liu, A., Humphreys, I.R., Turkarslan, S., Cutler, K.J., Arrieta-Ortiz, M.L., Li, Y., Radey, M.C., McLean, J.S., Cong, Q., Baker, D., Baliga, N.S., Peterson, S.B. & Mougous, J.D. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. https://doi.org/10.1016/j.cell.2023.08.017 Cell, Online Sept 7 2023
Hendrickson, E.L., Bor, B., Kerns, K.A., Cen, L., Shi, W., He, X., McLean J.S. 2023. Ultrasmall epibiont Nanosynbacter lyticus strain TM7x and host bacterial transcriptional activity after initial parasitism. J. Oral Microbiol. DOI: 10.1080/20002297.2023.2287349
2022
Liu, J., Utter, D.R., Nie, J., Kerns, K.A., Lamont, E.I., Hendrickson, E.L., Wang, X., McLean, J.S., He, X., Bor, B. (2022). Draft Genome Sequences of Nine “Candidatus Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity. Microbiology Resource Announcments: Vol. 11, No. 8. https://doi.org/10.1128/jb.00112-22
Cen, L., Chang, Y., Bedree, J.K., Ma, Y., Zhong, Q., Utter, D.R., Dong, P., Lux, R., Bor, B., Liu, J., McLean, J.S., Le, S., He, X. (2022). Exploitation of a Bacterium -Encoded Lytic Transglycosylase by a Human Oral Lytic Phage to Facilitate Infection. Journal of Virology: Vol 96, No. 17. https://doi.org/10.1128/jvi.01063-22
Hendrickson, E.L., Bor, B., Kerns, K.A., Lamont, E.I., Chang, Y., Liu, J., Cen, L., Schulte, F., Hardt, M., Shi, W., He, X., McLean, J.S. (2022). Transcriptome of Epibiont Saccharibacteria Nanosynbacter lyticus Strain TM7x During Establishment of Symbiosis. Journal of Bacteriology: Vol 204, No. 9. https://doi.org/10.1128/jb.00112-22
Nie, J., Utter, D.R., Kerns, K.A., Lamont, E.I., Hendrickson, E.L., Liu, J., Wu, T., He, X., McLean, J.S. & Bor, B. (2022). Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria. mSystems: e0148821. https://doi.org/10.1128/msystems.01488-21
Tian, J., Utter, D.R., Cen, L., Dong, P., Shi, W., Bor. B., Qin, M., McLean, J.S., & He, X. (2022). Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment. Proceedings of the National Academy of Sciences of the United States of America, 119(2), e2114909119. https://doi.org/10.1073/pnas.2114909119
2021
Chipashvili, Otari, Daniel R. Utter, Joseph K. Bedree, Yansong Ma, Fabian Schulte, Gabrielle Mascarin, Yasmin Alayyoubi, Deepak Chouhan, Markus Hardt, Felicitas Bidlack, Hatice Hasturk, Xuesong He, Jeffrey S. McLean, Batbileg Bor. Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation. Cell Host & Microbe 2021, ISSN 1931-3128, https://doi.org/10.1016/j.chom.2021.09.009. https://www.sciencedirect.com/science/article/pii/S193131282100425X
https://asm.org/Podcasts/TWiM/Episodes/Episymbionts-Are-Good-For-You-TWiM-254
Lamont, E.I., Gadkari, A., Kerns, K.A., To, T.T., Daubert, D., Kotsakis, G., Bor, B., He, X., McLean, J.S.* Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. Molecular Oral Microbiology. 2021 Nov 11. https://doi.org/10.1111/omi.12323 PubMed PMID: 33174294
TM7_G3_3_HMT_351_EL001 assembly accessible at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA663916
2020
Bor B, Collins AJ, Murugkar PP, Balasubramanian S, To TT, Hendrickson EL, Bedree JK, Bidlack FB, Johnston CD, Shi W, McLean JS, He X, Dewhirst FE. Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts. J Dent Res. 2020 Feb 19. https://doi.org/10.1177/0022034520905792. PubMed PMID: 32075512.
McLean, J.S.*, Bor, B., Kerns, K.A., Liu, Q., To, T.T., Solden, L., Hendrickson, E.L., Wrighton, K., Shi, W., and He, X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Reports 32. 2020 July 21. https://doi.org/10.1016/j.celrep.2020.107939 PubMed PMID: 32698001
Genomes G5, G3, G6, G1: Bioproject PRJNA38479 https://www.ncbi.nlm.nih.gov/bioproject/384792
Our work on nano-sized parasitic bacteria covered in TWiM episode 222
https://asm.org/Podcasts/TWiM/Episodes/Biosensors-in-bacteria-TWiM-222
Utter, D.R., He, X., Cavanaugh, C.M., McLean, J.S., Bor., B. The saccharibacterium TM7x elicits differential responses across its hosts range. ISME 2020 Aug 24. https://doi.org/10.1038/s41396-020-00736-6
Lamont, E.I., Hendrickson, E.L., McLean, J.S., He, X., Bor, B. Complete Genome Sequence of Strain BB001, a Novel Epibiont Bacterium from the Candidate Phylum Saccharibacteria (TM7) ASM. 2020 Aug 20. https://doi.org/10.1128/MRA.00810-20 PubMed PMID: 32816985
Bor B, Collins AJ, Murugkar PP, Balasubramanian S, To TT, Hendrickson EL, Bedree JK, Bidlack FB, Johnston CD, Shi W, McLean JS, He X, Dewhirst FE. Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts. J Dent Res. 2020 Feb 19. https://doi.org/10.1177/0022034520905792. PubMed PMID: 32075512
Lamont, E.I., Gadkari, A., Kerns, K.A., To, T.T., Daubert, D., Kotsakis, G., Bor, B., He, X., McLean, J.S. Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. Molecular Oral Microbiology. 2020 Nov 11. https://doi.org/10.1111/omi.12323 PubMed PMID: 33174294
TM7_G3_3_HMT_351_EL001 assembly accessible at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA663916
2019
Bor B, Bedree JK, Shi W, McLean JS, He X. Saccharibacteria (TM7) in the Human Oral Microbiome. J Dent Res. 2019 Mar 20:22034519831671. doi: 10.1177/0022034519831671. [Epub ahead of print] PubMed PMID: 30894042.
2018
Bor B, McLean JS, Foster KR, Cen L, To TT, Serrato-Guillen A, Dewhirst FE, Shi W, He X. Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12277-12282. doi: 10.1073/pnas.1810625115. Epub 2018 Nov 15. PubMed PMID: 30442671
McLean, J.S.* , Bor, B., To, T.T., Liu, Q., Kerns, K.A., Solden, L.M., Wrighton, K.C., He, X. & Shi, W. Independent Acquisition and Adaptation of Ultra-Small Bacteria with Reduced Genomes from the Phylum Saccharibacteria to Human Hosts. available as a preprint while under review at Cell (https://ssrn.com/abstract=3192029) BioProject Accession No : PRJNA384792
Bedree Joseph K, Batbileg Bor, Lujia Cen, Anna Edlund, Renate Lux, Jeffrey S. McLean, Wenyuan Shi and Xuesong He. Quorum Sensing Modulates the Epibiotic-Parasitic Relationship between Actinomyces odontolyticus and its Saccharibacteria epibiont, a Nanosynbacter lyticus strain, TM7x. Front. Microbiol. | doi: 10.3389/fmicb.2018.02049
Proposed NCBI Taxonomy for Saccharibacteria Groups and Novel Genomes
2016
McLean, J. S.*, Q. Liu, B. Bor, J. K. Bedree, L. Cen, M. Watling, T. T. To, R. E. Bumgarner, X. He and W. Shi (2016). “Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont.” Genome Announc 4(1) GenBank Accession No : LLVT00000000
2015
He, Xuesong#, McLean, Jeffrey S.#*(co-first author, co-corresponding author), Edlund, Anna, Yooseph, Shibu, Hall, Adam P., Liu, Su-Yang, Dorrestein, Pieter C., Esquenazi, Eduardo, Hunter, Ryan C., Cheng, Genhong, Nelson, Karen E., Lux, Renate, Shi, Wenyuan. (2015) Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences 112(1):244-249.
doi: 10.1073/pnas.1419038112. http://www.pnas.org/content/112/1/244.full OPEN ACCESS Genbank file for XH001 (note the annotations copied over from Actinomyces odontolyticus F0309 genome) BioProject Accession No : PRJNA241438
Bedree Joseph K, Batbileg Bor, Lujia Cen, Anna Edlund, Renate Lux, Jeffrey S. McLean, Wenyuan Shi and Xuesong He. Quorum Sensing Modulates the Epibiotic-Parasitic Relationship between Actinomyces odontolyticus and its Saccharibacteria epibiont, a Nanosynbacter lyticus strain, TM7x. Microbiol. | doi: 10.3389/fmicb.2018.02049
Bor B, Poweleit N, Bois JS, Cen L, Bedree JK, Zhou ZH, Gunsalus RP, Lux R, McLean JS, He X, Shi W. 2015. Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces. Microb Ecol doi:10.1007/s00248-015-0711-7:1-13. http://link.springer.com/article/10.1007%2Fs00248-015-0711-7# GenBank Accession No : CP007496
2013
McLean, JS*, M.-J. Lombardo, J. H. Badger, A. Edlund, M. Novotny, J. Yee-Greenbaum, N. Vyahhi, A. P. Hall, Youngik Yang, C. L. Dupont, M. G. Ziegler, H. Chitsaz, A. E. Allen, S. Yooseph, G. Tesler, P. Pevzner, R. Friedman, K. H. Nealson, J. C. Venter and R. S. Lasken (2013). “Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.” PNAS. Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110
PMCID: PMC3696752 http://www.pnas.org/content/110/26/E2390.full BioProject Accession No : PRJNA193445 GenBank Accession No : KF057992
