Candidatus savagella
1. Classification
a. Higher order taxa
Domain: Bacteria Phylum: Firmicutes Class: Clostridia Order: Clostridiales Family: Clostridiaceae Species: candidatus savagella
2. Description and significance
Describe the appearance, habitat, etc. of the organism, and why you think it is important.
- Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*
3. Genome structure
SFB are associated with the family Clostridiaceae but diverged early in evolution from the family [1]. SFB has a small genome that encodes a single circular chromosome with a low Guanine-Cytosine (GC) content. [1,4,7]. About 78% of protein-coding genes are like other Clostridia or Firmicutes, but 8.6% of proteins have no orthologues. SFB has four clusters of SFB-specific proteins that are not found in other bacteria and further distinguishes SFB from the Clostridiaceae family. Cluster one and three are proteins that are part of the surface structures that are relevant to environment adaptation. Yet, little is known about clusters two and four [1]. These SFB-specific proteins have variations in DNA sequence that may be relevant to host selectivity [1]. SFB lack genes responsible for synthesis of nutrients such as vitamins, amino acids, nucleotides, and cofactors. Therefore, SFB are between obligate and facultative symbionts [1,4]. SFB have several genes involved in the transport of small molecules and ions across the cell membrane and have various extracellular proteases that assist in degrading host and dietary proteins. SFB have an anaerobic metabolism and require vitamins, cofactors, and amino acids from the environment to maintain their cellular processes [1,4]. Like other bacteria, SFB have high numbers of genes that code for cell cycle control, cell differentiation, cell shape, the release of holdfasts and spores from filament and the elimination of cytoplasmic proteins [1]. Moreover, SFB are subject to foreign invading DNA through horizontal gene transfer [1,4]. Yet, SFB has an important protein responsible for membrane remodeling, endocytosis, and cell morphology and the making of holdfast cells required for making a strong host-microbe interaction [1,4]. SFB also has genes that encode for flagella [1,4].
4. Cell structure
Interesting features of cell structure. Can be combined with “metabolic processes”
5. Metabolic processes
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).
6. Ecology
Habitat; symbiosis; contributions to the environment.
7. Pathology
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
8. Current Research
Include information about how this microbe (or related microbes) are currently being studied and for what purpose
9. References
[1] [Pamp, S. J., Harrington, E. D., Quake, S. R., Relman, D. A., & Blainey, P. C. (2012). Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research, 22(6), 1107–1119. https://doi.org/10.1101/gr.131482.111]
[2] [Clostridium. (2010). In MicrobeWiki. https://microbewiki.kenyon.edu/index.php?title=Clostridium&oldid=54377]
[3] [Jonsson, H. (2013). Segmented filamentous bacteria in human ileostomy samples after high-fiber intake. FEMS Microbiology Letters, 342(1), 24–29. https://doi.org/10.1111/1574-6968.12103]
[4] [Ericsson, A. C., Hagan, C. E., Davis, D. J., & Franklin, C. L. (2014). Segmented filamentous bacteria: commensal microbes with potential effects on research. Comparative Medicine, 64(2), 90–98]
[5] [Jonsson, H., Hugerth, L.W., Sundh, J. et al. Genome sequence of segmented filamentous bacteria present in the human intestine. Commun Biol 3, 485 (2020). https://doi.org/10.1038/s42003-020-01214-7]
[6] [Wolfe AE, Moskowitz JE, Franklin CL, Wiemken TL, Ericsson AC (2020) Interactions of Segmented Filamentous Bacteria (Candidatus Savagella) and bacterial drivers in colitis-associated colorectal cancer development. PLoS ONE 15(7): e0236595. https://doi.org/10.1371/journal.Pone.0236595]
[7] [Gaboriau-Routhiau, V., Rakotobe, S., Lecuyer, E., Mulder, I., Lan, A., Bridonneau, C., et al. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31, 677–689. doi: 10.1016/j.immuni.2009.08.020]
[8] [Thompson, C. L., Vier, R., Mikaelyan, A., Wienemann, T., & Brune, A. (2012). ‘Candidatus Arthromitus’ revised: Segmented filamentous bacteria in arthropod guts are members of Lachnospiraceae. Environmental Microbiology, 14(6), 1454–1465. https://doi.org/10.1111/j.1462-2920.2012.02731.x]
[9] [Kuwahara, T., Ogura, Y., Oshima, K., Kurokawa, K., Ooka, T., Hirakawa, H., Itoh, T., Nakayama-Imaohji, H., Ichimura, M., Itoh, K., Ishifune, C., Maekawa, Y., Yasutomo, K., Hattori, M., & Hayashi, T. (2011). The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing. DNA Research, 18(4), 291–303. https://doi.org/10.1093/dnares/dsr022]
[10] [Desvaux, M. (2005). Clostridium cellulolyticum: Model organism of mesophilic cellulolytic clostridia. FEMS Microbiology Reviews, 29(4), 741–764. https://doi.org/10.1016/j.femsre.2004.11.003]
[11] [Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A., & Setoyama, H. (1995). Segmented Filamentous Bacteria Are Indigenous Intestinal Bacteria That Activate Intraepithelial Lymphocytes and Induce MHC Class II Molecules and Fucosyl Asialo GM1 Glycolipids on the Small Intestinal Epithelial Cells in the Ex-Germ-Free Mouse. Microbiology and Immunology, 39(8), 555–562. https://doi.org/10.1111/j.1348-0421.1995.tb02242.x]
[12] [Klaasen, H. L. B. M., Koopman, J. P., Poelma, F. G. J., & Beynen, A. C. (1992). Intestinal, segmented, filamentous bacteria. FEMS Microbiology Reviews, 8(3–4), 165–179. https://doi.org/10.1111/j.1574-6968.1992.tb04986.x]
[13] [Klaasen, H. L., Van der Heijden, P. J., Stok, W., Poelma, F. G., Koopman, J. P., Van den Brink, M. E., Bakker, M. H., Eling, W. M., & Beynen, A. C. (1993). Apathogenic, intestinal, segmented, filamentous bacteria stimulate the mucosal immune system of mice. Infection and Immunity, 61(1), 303–306. https://doi.org/10.1128/iai.61.1.303-306.1993]
[14] [Gaboriau-Routhiau, V., Rakotobe, S., Lecuyer, E., Mulder, I., Lan, A., Bridonneau, C., et al. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31, 677–689. doi: 10.1016/j.immuni.2009.08.020]
[15] [Yin, Y., Wang, Y., Zhu, L., Liu, W., Liao, N., Jiang, M., et al. (2013). Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens. ISME J. 7, 615–621. doi: 10.1038/ismej.2012.128]
