Genome Announcements

• To TT, Liu Q, Watling M, Darveau RP, Bumgarner RE, McLean JS. Genome sequence of low-passage clinical isolate Porphyromonas gingivalis MP4-504. Genome Announcements

• 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).

• McLean, J. S.*, Q. Liu, J. Thompson, A. Edlund and S. Kelley (2015). "Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients." Genome Announc 3(6)

• 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

• 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#

• 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.

• He X, McLean JS, Edlund A, et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci U S A. 2015;112(1):244-249. doi:10.1073/pnas.1419038112.

  Reviews

  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.

Proposed NCBI Taxonomy for Saccharibacteria Groups and Novel Genomes

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. (2020). Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Reports 32.

https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30920-7

Genomes

https://www.ncbi.nlm.nih.gov/bioproject/384792

Independent acquisition and adaptation to human hosts is evident in the diversity across phylum Saccharibacteria which share reduced genomes and ultra-small cells

Published preprint BioRxiv online Feb 2, 2018, DOI: 10.1101/258137

Group

Accession
Organism
New NCBI Taxonomy

GENOME DEPOSITIONS

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA384792

Registration date: 5-Feb-2019
University of Washington

G1 Genus Nanosynbacter

TM7x

Nanosynbacter Lyticus Type_Strain_TM7x HOT_952

Nanosynbacter lyticus strain TM7x Genome

 https://www.ncbi.nlm.nih.gov/nuccore/CP007496.1/

 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000803625.1/

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Saccharimonia; Nanosynbacterales; Nanosynbacteraceae; Nanosynbacter; Nanosynbacter Lyticus Type_Strain_TM7x HOT_952

Etymology:

“Nanosynbacterales ord. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

L. fem. n. bacterium, bacterium: n. bacterium

Nanosynbacterales reflects the ultra-small, synergist symbiotic relationship with a host for this class of TM7.

“Nanosynbacteraceae fam. nov.,”

N.L. fem. pl. n. Nanosynbacteraceae, -aceae ending to denote a family, the family-level lineage of

genus Nanosynbacter. Description is the same as the order Nanosynbacterales.

“Nanosynbacter gen. nov.”

N.L. fem. n. Nanosynbacter, -er ending is to denote a genus. Description is the same as the order

Nanosynbacterales.

“ lyticus sp. nov.”

L. fem. n. lysis, adj. lytic to reflect the ability of this isolated strain to lyse its host

“lyticus type strain TM7x sp. nov.,”

N.L. fem. n. lyticus to reflect the manner in which this isolated strain lysis its host Actinomyces odontolyticus subsp. actinosynbacter strain XH001.

 PQNZ00000000
   Candidatus Saccharibacteria bacterium TM7_ANC_G1_1
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Saccharimonia; (Ca.) Saccharimonales; (Ca.)   Sacchiramonaceaea; (Ca.) Nanosynbacter; (Ca.) Nanosynbacter sp.  TM7_ANC_38.39_G1_1

PQOA00000000
   Candidatus Saccharibacteria bacterium TM7_G1_3_12A
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Saccharimonia; (Ca.) Nanosynbacterales;
   (Ca.) Nanosynbacteraceae; (Ca.) Nanosynbacter; (Ca.) Nanosynbacter sp.  TM7_G1_3_12A

G3
PRLL00000000
   Candidatus Saccharibacteria bacterium TM7_KMM_G3_1_HOT_351
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Nanosyncoccalia; (Ca.) Nanosyncoccales; (Ca.) Nanosyncoccacae;
   (Ca.) Nanosyncoccus; (Ca.) Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351
PRLM00000000
   Candidatus Saccharibacteria bacterium TM7_G3_2_Rum_HOT_351B
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Nanosyncoccalia, (Ca.) Nanosyncoccales; (Ca.) Nanosyncoccacae;
   (Ca.) Nanosyncoccus; (Ca.) Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B

G5

PRLN00000000
   Candidatus Saccharibacteria bacterium TM7_ EAM_G5_2_HOT_356
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Nanoperiomorbia; (Ca.) Nanoperiomorbales;
   (Ca.) Nanoperiomorbaceae; (Ca.) Nanoperiomorbus; (Ca.) Nanoperiomorbus periodonticus TM7_EAM_G5_2_HOT_356

PRLO00000000
   Candidatus Saccharibacteria bacterium TM7_ EAM_G5_1_HOT_356
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Nanoperiomorbia; (Ca.) Nanoperiomorbales;
   (Ca.) Nanoperiomorbaceae; (Ca.)  Nanoperiomorbus; (Ca.) Nanoperiomorbus periodonticus TM7_EAM_G5_1_HOT_356

G6
PRLK00000000
   Candidatus Saccharibacteria bacterium TM7_CMJM_G6_1_HOT_870
   cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla;
   Candidatus Saccharibacteria; (Ca.) Nanosyncoccalia; (Ca.)  Nanogingivales; (Ca.) Nanogingivalaceae;
    (Ca.) Nanogingivalis; (Ca.) Nanogingivalis gingiviticus TM7_CMJM_G6_1_HOT_870

Text S1. Proposed Etymology of TM7 proposed classifications

Type, Kingdom, Phylum, Class, Order, Family, Genus, Species – Isolation source

G5 Genus Nanoperiomorbus

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Nanoperiomorbia, Nanoperiomorbales; Nanoperiomorbaceae; Nanoperiomorbus; Nanoperiomorbus periodonticus TM7_ EAM_G5_1_HOT_356

“Nanoperiomorbia class. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacterium.

N.L. fem. pl. n. peri-odon, periodontal: n. perio reflects a biological niche of TM7

1. fem. pl. n. morbidus, morbid: n. morbid reflects the resulting tissues morbidity in the presence of TM7.

• “Nanoperiomorbia nov.,” N.L. fem. pl. n. Nanoperiomorbia to reflect the ultra-small size, biological niche in which the sample was isolated, and resulting morbidity of host tissue for this class of TM7.

“Nanoperiomorbales ord. nov.”

• “Nanoperiomorbales nov.,” N.L. fem. pl. n. Nanoperiomorbales, –ales ending to denote an order, the order-level lineage of genus Nanoperiomorbus. Description is the same as the class Nanoperiomorbia.

“Nanoperiomorbaceae fam. nov.”

• “Nanoperiomorbaceae nov.,” N.L. fem. pl. n. Nanoperiomorbaceae, –aceae ending to denote a family, the family-level lineage of genus Nanoperiomorbus. Description is the same as the class Nanoperiomorbia.

“Nanoperiomorbus gen. nov.”

• “Nanoperiomorbus nov.,” N.L. fem. n. Nanoperiomorbus, –us ending to denote a genus. Description is the same as the class Nanoperiomorbia.

“periodonticus sp. nov.”

1. fem. n. peri-odon, periodontal: n. periodontal literally means “around the tooth” and reflects the sources from which this species of TM7 was isolated.

• “periodonticus nov.,” N.L. fem. n. periodonticus to reflect the isolation source of this TM7 species.

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Nanoperiomorbia; Nanoperiomorbales; Nanoperiomorbaceae; Nanoperiomorbus; Nanoperiomorbus periodonticus TM7_ EAM_G5_2_HOT_356

“Nanoperiomorbia class. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacterium.

N.L. fem. pl. n. peri-odon, periodontal: n. perio reflects a biological niche of TM7

1. fem. pl. n. morbidus, morbid: n. morbid reflects the resulting tissues morbidity in the presence of TM7.

• “Nanoperiomorbia nov.,” N.L. fem. pl. n. Nanoperiomorbia to reflect the ultra-small size, biological niche in which the sample was isolated, and resulting morbidity of host tissue for this class of TM7.

“Nanoperiomorbales ord. nov.”

• “Nanoperiomorbales nov.,” N.L. fem. pl. n. Nanoperiomorbales, –ales ending to denote an order, the order-level lineage of genus Nanoperiomorbus. Description is the same as the class Nanoperiomorbia.

“Nanoperiomorbaceae fam. nov.”

• “Nanoperiomorbaceae nov.,” N.L. fem. pl. n. Nanoperiomorbaceae, –aceae ending to denote a family, the family-level lineage of genus Nanoperiomorbus. Description is the same as the class Nanoperiomorbia.

“Nanoperiomorbus gen. nov.”

• “Nanoperiomorbus nov.,” N.L. fem. n. Nanoperiomorbus, –us ending to denote a genus. Description is the same as the class Nanoperiomorbia.

“periodonticus sp. nov.”

1. fem. n. peri-odon, periodontal: n. periodontal literally means “around the tooth” and reflects the sources from which this species of TM7 was isolated.

• “periodonticus nov.,” N.L. fem. n. periodonticus to reflect the isolation source of this TM7 species.

G3 Genus Nanosyncoccus

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Nanosyncoccalia, Nanosyncoccales; Nanosyncoccacae; Nanosyncoccus; Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B

“Nanosyncoccalia class. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

1. fem. pl. n. coccus, cocci: n. cocci reflects the spherical shape of the bacterium

• “Nanosyncoccalia nov.,” N.L. fem. pl. n. Nanosyncoccalia to reflect the ultra-small size, synergist symbiotic relationship with a host, and the spherical shape of this class of TM7.

“Nanosyncoccales ord. nov.”

• “Nanosyncoccales nov.,” N.L. fem. pl. n. Nanosyncoccales, –ales ending to denote an order, the order-level lineage of genus Nanosyncoccus. Description is the same as the class Nanosyncoccalia.

“Nanosyncoccaceae fam. nov.”

• “Nanosyncoccaceae nov.,” N.L. fem. pl. n. Nanosyncoccaceae, –aceae ending to denote a family, the family-level lineage of genus Nanosyncoccus. Description is the same as the class Nanosyncoccalia.

“Nanosyncoccus gen. nov.”

• “Nanosyncoccus nov.,” N.L. fem. n. Nanosyncoccus, -us ending to denote a genus. Description is the same as the class Nanosyncoccalia.

“alces sp. nov.”

1. fem. n. alces, moose: n. moose reflects the moose rumen from which this species of TM7 was isolated.

• “alces nov.,” N.L. fem. n. alces reflects the isolation source of this TM7 species.

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Nanosyncoccalia; Nanosyncoccales; Nanosyncoccacae; Nanosyncoccus; Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351

“Nanosyncoccalia class. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

1. fem. pl. n. coccus, cocci: n. cocci reflects the spherical shape of the bacterium

• “Nanosyncoccalia nov.,” N.L. fem. pl. n. Nanosyncoccalia to reflect the ultra-small size, synergist symbiotic relationship with a host, and the spherical shape of this class of TM7.

“Nanosyncoccales ord. nov.”

• “Nanosyncoccales nov.,” N.L. fem. pl. n. Nanosyncoccales, –ales ending to denote an order, the order-level lineage of genus Nanosyncoccus. Description is the same as the class Nanosyncoccalia.

“Nanosyncoccaceae fam. nov.”

• “Nanosyncoccaceae nov.,” N.L. fem. pl. n. Nanosyncoccaceae, –aceae ending to denote a family, the family-level lineage of genus Nanosyncoccus. Description is the same as the class Nanosyncoccalia.

“Nanosyncoccus gen. nov.”

• “Nanosyncoccus nov.,” N.L. fem. n. Nanosyncoccus, -us ending to denote a genus. Description is the same as the class Nanosyncoccalia.

“nanoralicus sp. nov.”

N.L. fem. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

1. fem. n. oralis, oral: n. oral to reflect the human oral cavity in which this species of TM7 was isolated.

• “nanoralicus nov.,” N.L. fem. n. nanoralicus reflects the ultra-small size and isolation sources of this TM7 species.

• 
  

G6 Genus Nanogingivalis

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Nanosyncoccalia; Nanogingivales; Nanogingivalaceae; Nanogingivalis; Nanogingivalis gingivitcus TM7_CMJM_G6_1_HOT_870

“Nanosyncoccalia class. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

1. fem. pl. n. coccus, cocci: n. cocci reflects the spherical shape of the bacterium

• “Nanosyncoccalia nov.,” N.L. fem. pl. n. Nanosyncoccalia to reflect the ultra-small size, synergist symbiotic relationship with a host, and the spherical shape of this class of TM7.

 “Nanogingivales ord. nov.”

• “Nanogingivales nov.,” N.L. fem. pl. n. Nanogingivales, –ales ending to denote an order, the order-level lineage of genus Nanogingivalis. Description is the same as the class Nanosyncoccalia.

“Nanogingivalaceae fam. nov.”

• “Nanogingivalaceae nov.,” N.L. fem. pl. n. Nanogingivalaceae, –aceae ending to denote a family, the family-level lineage of genus Nanogingivalis. Description is the same as the class Nanosyncoccalia.

“Nanogingivitcus gen. nov.”

• “Nanogingivalis nov.,” N.L. fem. n. Nanogingivitcus, –is ending to denote a genus. Description is the same as the class Nanosyncoccalia.

“gingivitcus sp. nov.”

1. fem. adj. gingivae, gingival: adj. gingival to reflect the tissue in which this species of TM7 was isolated.

• “gingivitcus nov.,” N.L. fem. n. gingivitcus reflects the isolation source of this TM7 species.

G1 Genus Nanosynsacchari

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Saccharimonia; Saccharimonales; Sacchiramonaceaea; Nanosynsacchari; Nanosynsacchari sp.  TM7_ANC_38.39_G1_1

 “Nanosynbacter gen. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

1. fem. n. bacterium, bacterium: n. bacterium

• “Nanosynbsacchari gen. nov.,” N.L. fem. n. Nanosynsacchari to reflect the ultra-small size and synergist symbiotic relationship with a host for this genus of TM7

cellular organisms; Bacteria; unclassified Bacteria; Bacteria candidate phyla; Candidatus Saccharibacteria; Saccharimonia; Saccharimonales; Sacchiramonaceaea; Nanosynsacchari; Nanosynsacchari sp.  TM7_G1_3_12A

 “Nanosynbacter gen. nov.”

N.L. fem. pl. n. nanos, nano: n. nano to reflect the ultra-small size of the TM7 bacteria.

N.L. fem. pl. n. synergia, synergy: n. synergy reflects synergistic and symbiotic relationship between TM7 and its host.

1. fem. n. bacterium, bacterium: n. bacterium

• “Nanosynbsacchari gen. nov.,” N.L. fem. n. Nanosynsacchari to reflect the ultra-small size and synergist symbiotic relationship with a host for this genus of TM7