Modulibacteria

Modulibacteria is a bacterial phylum formerly known as KS3B3 or GN06. It is a candidate phylum, meaning there are no cultured representatives of this group. Members of the Modulibacteria phylum are known to cause fatal filament overgrowth (bulking) in high-rate industrial anaerobic wastewater treatment bioreactors.[1][2]

Modulibacteria
Scientific classification
Domain:
Bacteria
Phylum:
"Modulibacteria"
Class:
"Moduliflexia"
Order:
"Moduliflexales"
Family:
"Moduliflexaceae"

Sekiguchi et al. 2015
Genus
  • "Ca. Moduliflexus"
  • "Ca. Vecturithrix"

The Modulibacteria phylum was first proposed in 2006 by two independent research groups based on analyses of 16S rRNA gene sequences. One group recovered Modulibacteria sequences from the a hypersaline microbial mat from Guerrero Negro (Baja California Sur, Mexico) and used the provisional name GN06 for the novel phylum,[3] while the other recovered sequences from sulfur-rich black mud marine sediments (CA, USA) and used the provisional name KSB3.[4]

The first genomic insights into the phylum were achieved in 2015, at which time the name "Modulibacteria" was proposed.[5] Two genomes were recovered from methanogenic sludge samples of a full-scale upflow anaerobic sludge blanket (UASB) reactor treating a high-strength organic wastewater discharged from a food-processing factory.

Through a combination of genome-based metabolic reconstruction and microscopic observation, it was determined that the two studied Modulibacteria species (Moduliflexus flocculans and Vecturithrix granuli) produce filamentous structures and are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility. Both have an unusually large number of sensory and response regulator genes compared to other bacteria.[5]

Members of the Modulibacteria phylum have been detected in a variety of environments in addition to bioreactors and hypersaline mats, such as wetland sediments (FJ516883.1), the dolphin mouth,[6][7] and a tubeworm from a coldseep (FM165273).

Taxonomy

The following taxonomy was proposed by Sekiguchi et al. 2015.[5][8] Phylogeny by Annotree v1.2.0[9][10] which uses the GTDB 05-RS95 (Genome Taxonomy Database)[11][12]

  • Class "Moduliflexia" Sekiguchi et al. 2015 ["Vecturitrichia" Sekiguchi et al. 2015]
    • Order "Moduliflexales" Sekiguchi et al. 2015 ["Vecturatrichales" Sekiguchi et al. 2015]
      • Family "Moduliflexaceae" Sekiguchi et al. 2015 ["Vecturatrichaceae" Sekiguchi et al. 2015]
        • Genus "Candidatus Moduliflexus" Sekiguchi et al. 2015[13]
          • Species "Ca. M. flocculans" Sekiguchi et al. 2015
        • Genus "Candidatus Vecturithrix" Sekiguchi et al. 2015[14]
          • Species "Ca. V. granuli" Sekiguchi et al. 2015

References
  1. Yamada, Takeshi; Yamauchi, Toshihiro; Shiraishi, Koji; Hugenholtz, Philip; Ohashi, Akiyoshi; Harada, Hideki; Kamagata, Yoichi; Nakamura, Kazunori; Sekiguchi, Yuji (2007-05-31). "Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges". The ISME Journal. 1 (3): 246–255. doi:10.1038/ismej.2007.28. ISSN 1751-7362. PMID 18043635. S2CID 5077407.
  2. Yamada, Takeshi; Kikuchi, Kae; Yamauchi, Toshihiro; Shiraishi, Koji; Ito, Tsukasa; Okabe, Satoshi; Hiraishi, Akira; Ohashi, Akiyoshi; Harada, Hideki; Kamagata, Yoichi; Nakamura, Kazunori (2011-01-21). "Ecophysiology of Uncultured Filamentous Anaerobes Belonging to the Phylum KSB3 That Cause Bulking in Methanogenic Granular Sludge". Applied and Environmental Microbiology. 77 (6): 2081–2087. Bibcode:2011ApEnM..77.2081Y. doi:10.1128/aem.02475-10. ISSN 0099-2240. PMC 3067334. PMID 21257808.
  3. Ley, Ruth E.; Harris, J. Kirk; Wilcox, Joshua; Spear, John R.; Miller, Scott R.; Bebout, Brad M.; Maresca, Julia A.; Bryant, Donald A.; Sogin, Mitchell L.; Pace, Norman R. (2006-05-01). "Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat". Applied and Environmental Microbiology. 72 (5): 3685–3695. Bibcode:2006ApEnM..72.3685L. doi:10.1128/AEM.72.5.3685-3695.2006. ISSN 0099-2240. PMC 1472358. PMID 16672518.
  4. Tanner, Michael (2006). "Complex Microbial Communities Inhabiting Sulfide-rich Black Mud from Marine Coastal Environments". Biotechnology et Alia. 8: 1–16.
  5. Sekiguchi, Yuji; Ohashi, Akiko; Parks, Donovan H.; Yamauchi, Toshihiro; Tyson, Gene W.; Hugenholtz, Philip (2015-01-27). "First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking". PeerJ. 3: e740. doi:10.7717/peerj.740. ISSN 2167-8359. PMC 4312070. PMID 25650158.
  6. Bik, Elisabeth M.; Costello, Elizabeth K.; Switzer, Alexandra D.; Callahan, Benjamin J.; Holmes, Susan P.; Wells, Randall S.; Carlin, Kevin P.; Jensen, Eric D.; Venn-Watson, Stephanie; Relman, David A. (2016-02-03). "Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea". Nature Communications. 7 (1): 10516. Bibcode:2016NatCo...710516B. doi:10.1038/ncomms10516. ISSN 2041-1723. PMC 4742810. PMID 26839246.
  7. Dudek, Natasha K.; Sun, Christine L.; Burstein, David; Kantor, Rose S.; Aliaga Goltsman, Daniela S.; Bik, Elisabeth M.; Thomas, Brian C.; Banfield, Jillian F.; Relman, David A. (2017-12-18). "Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome". Current Biology. 27 (24): 3752–3762.e6. doi:10.1016/j.cub.2017.10.040. ISSN 1879-0445. PMID 29153320.
  8. Euzéby JP. ""Modulibacteria"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  9. "AnnoTree v1.2.0". AnnoTree.
  10. Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47 (9): 4442–4448. doi:10.1093/nar/gkz246. PMC 6511854. PMID 31081040.
  11. "GTDB release 05-RS95". Genome Taxonomy Database.
  12. Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
  13. Sayers. "Moduliflexus". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
  14. Sayers. "Vecturithrix". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
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