Joshua Monteith, Bench A, 18/10/2017, MICR3004.
Higher order taxa
Bacteria – Firmicutes – Clostridia– Clostridiales – Clostridiales Family XIII. Incertae Sedis – Mogibacterium
Mogibacterium timidum, ATCC 3309, formerly known as Eubacterium timidum.
Description and Significance
The species Mogibacterium timidum (formerly Eubacterium timidum) is an obligately anaerobic, non-spore forming, gram-positive bacteria. The species was first isolated from a bacterial flora study by Holdeman and colleagues of adult individuals with periodontitis in 1980 .
Since its discovery, M. timidum has been noted in many studies due to its increased incidence in adult periodontitis, and other diseased regions of the neck, head and lungs . However, many other microbial studies have found its presence alongside persons infected with Mycobacterium tuberculosis, high methane production in ruminant livestock, human peritoneal fluid and human necrotizing fasciitis in the thigh regions . Despite its increased presence within the microbial community of diseased and negatively impacting health conditions, the mechanisms by which M. timidum are pathogenic or pathobionts are largely unknown .
The most characterized strain, the initially discovered M. timidum ATCC 33093 was found to have a circular genome 1,806,210 base pairs long with a G+C content of 44.3%. The genome includes 1,657 coding genes and 49 small, non-coding genes resulting in a total of 1705 transcripts. There are currently no plasmids documented to be commonly found within these species .
Cell Structure and Metabolism
M. timidum is described as a gram-positive rod organism, slightly diptheroid in shape with the presence of a thick layer of peptidoglycan within the cell wall . The organism is named after the latin adjective timidum translating to timid or fearful due to its slow growth in clumps in culture. The organism also has been noted to be a biolfilm non-producer in endodontic infections .
Initially, the species was classified under the genus Eubacterium after its discovery, due to its negative metabolic characteristics . Historically, the Eubacterium genus has acted as a repository for bacteria which cannot be classified within the phenotypically defined genera such as Actinomyces to which is closely resembles, Bifidobacterium, Lactobacillus and Propionibacterium . When cultured in peptone-yeast-glucose medium, the organism was found to only produce phenyl-acetate its sole metabolic end product and could not undergo arginine hydrolysis or nitrate reduction . The phenotypic characterisation of the initial M. timidum strains discovered by Holdeman et al. were also found to be:
- Unable to hydrolyse starch and esculin
- Unable to produce indole or catalase
- Unable to digest gelatin, milk and meat
- Unable to produce acid from amygdalin, arabinose, cellobiose, erythritol, esculin, fructose, glucose, glycogen, inositol, lactose, maltose, mannitol, mannose, melezitose, melibiose, raffinoise, rhamnose, riboise, salicin, sorbitol, starch, sucrose, trehalose, and xylose.
- Unable to ferment adonitol, dextrin, dulcitol, galactose, glycerol, sorbose and pectin.
- Unable to utilize pyruvate or lactate.
- Trace elements of acetate, formate and succinate were detected in M. timidum culture
- On egg yolk agar – where it is best cultured – lecithinase and lipase are not produced.
- Unable to produce butyric acid and branched chain acids
- Unable to ferment carbohydrates (which differentiated the species from its morphologically similar genus Actinomyces.
It is due to the limited metabolic ability of M. timidum and its obligate anaerobic growth that the species is found to be slow growing, and difficult to culture.
Further studies since its discovery attempted to reassign the former Eubacterium timidum to a new genus Mogibacterium confirmed the species’ inability to undergo arginine hydrolysis or nitrate reduction, producing the sole metabolic end product of phenyl-acetate .The formation of the new genus was also to facilitate two newly discovered bacteria M. pumilim and M. vescum with phenotypically and phylogenetically similar profiles to M. timidum .
The organism is an obligate anaerobe, and has been unable to be cultured within media that is aerobic . The species is well noted within many studies to be found within the oral cavity residing at highest abundance within deep periodontal pockets, infected pulp and carious dentine of humans . The species has found to persist within subgingival regions of the oral cavity due to the anaerobic environment, and has shown to be less abundant in supragingival regions due to increased chemomechanical factors such as tooth-brushing, the use of floss and competition from the microbial environment .
Although a large body of literature surrounding the relative abundance of M. timidum is linked to periodontitis and other endodontic infections, M. timidum has also been isolated in other various human samples. This species has been isolated within samples from infected sinus, buccal abscess/cellulitis, Ludwig’s angina, parotid gland abscess, lung aspirate, peritoneal fluid, blood and necrotizing fasciitis of the groin .
Further studies have also found M. timidum to be markedly present within ruminant livestock which were high emitters of methane. Although this species, along with the also asaccharolytic Pyramidobacter, was found to be enriched in high methane emitting livestock, it is still unclear why M. timidum and its metabolic capabilities was present in this subset of cattle .
Studies conducted in 2015 by Marchesan and colleagues discovered that M. timidum is closely associated within the oral microbial community with various other species known to correlate with periodontitis. This community predominately led by Synergistes and Spirochaetes also was found to contain pathogenic and pathobiont species such as Porphyromonas gingivalis, Tannerell forsythia, Eubacterium nodatum, Eubacteria saphenum, Fretibacterium fastidiosum, Fusobacterium nucleatum, Prevotella intermedia and M. timidum. The study also discovered two compounds known as cyclocipeptides which predicted to serve as quorum-sensing or bacteriocidal molecules which may play a role in periodontal biofilm dysbiosis. This dysbiosis may cause persistence and disease exarcerbation, along with the growth of the bacterial communities associated with M. timidum .
Although the relationships with clinical pathologies in association with M. timidum are well understood, there is currently no evidence which can differentiate the role of M. timidum as an pathobiont organism which cultivates well alongside pathogenic microorganisms or a pathogenic organism in which virulence factors act on the diseased host .
Despite this, M. timidum has shown not only an increase by up to 4.8x in subgingival tissue of chronic periodontitis suffers, yet hosts also have increased serum Immunoglobulin A levels produced in the case of adult refractory periodontitis . This suggests the organism has sufficiently breached host defenses to stimulate the immune response .
A study on a cohort of Hong-Kong Chinese individuals have also linked the presence of M. timidum within the sputum to patients infected with Mycobacterium tuberculosis, finding although M. timidum had a low relative abundance within sputum samples, there was a marked increase in the relative abundance of the species in disease state, where it was hypothesized that M. timidum may affect the dynamics of the microbial community and clinical outcomes .
A further study by Casarin and colleagues in 2012 investigated the frequency of detection of M. timidum between chronic and aggressive periodontitis suffering individuals with Type II Diabetes Mellitus [T2DM]. The study found that patients with chronic periodontitis presented with a higher relative abundance of M. timidum than those with aggressive periodontitis in both T2DM and healthy patients. The study also found that the relative abundance of M. timidum is highest in those with severe, uncontrolled T2DM. Although this study aimed to correlate the glycemic control of the host in relation to the inflammation and subgingival microbial profile, it found no correlation with blood-glucose levels and M. timidum infection .
The study further found M. timidum was almost absent at healthy sites within the oral cavity, and suggests that more knowledge surrounding the pathogenicity and virulence factors of the organism is needed to define its role within sites exhibiting periodontal breakdown .
Application to biotechnology
As of 2014, the ATCC 33093 strain of M. timidum cultured in peptone-yeast-glucose broth was found to be resistant to tetracycline and doxycycline at minimum inhibitory concentrations of 4mg/L, and 3mg/mL respectively .
- In 2012, Casarin and colleagues found that patients with chronic periodontitis presented with a higher relative abundance of M. timidum than those with aggressive periodontitis in both diabetic and non-diabetic patients. The study also found that that the relative abundance of M. timidum is highest in those with severe, uncontrolled Diabetes Mellitus .
- In 2013, Cheung and colleagues discovered the increased presence of M. timidum within the sputum microbial community of Hong Kong Chinese patients infected with M. tuberculosis.
- In 2014, Al-Ahmad and colleagues discovered that M. timidum is resistant to tetracycline and doxycycline, and also does not produce biofilm within human subginginval infections .
- In 2015, Wallace and colleagues discovered the increased presence of M. timidum within the rumen microbial community of high-methane emitting livestock .
- Holdeman, J., Cato, E., Burmeister, W., & Moore. (1980). Descriptions of Eubacterium timidum sp. nov., Eubacterium brachy sp. nov., and Eubacterium nodatum sp. nov. isolated from human periodontitis. Int J Syst Evol Microbiol 30: 163-169.
- Nakazawa, F., Sato, M., Poco, S. E., Hashimura, T., Ikeda, T., Kalfas, S., Sundqvist, G., & Hoshino E. (2000). Description of Mogibacterium pumilium gen. nov., sp. Nov. and Mogibacterium vescum gen. nove., sp. Nov., and reclassification of Eubacterium timidum (Holdeman et al. 1980) as Mogibacterium timidum gen. nov., comb. nov. Int J Syst Evol Microbiol 50: 679-688.
- Hill, G.B., Ayers, O.M., & Kohan, A.P. (1987). Characteristics and sites of infection of Eubacterium nodatum, Eubacterium timidum and Eubacterium brachy, and other assaccharolytic eubacteria. J Clin Microbiol 25: 1540-1545.
- Cheung, M.K., Lam, W.y., Fung, W.Y., Law, P.T.W., Au, C.H., Nong, W., Kam, K.M., Kwan, H.S., & Tsui, S.K. (2013) Sputum Microbiota in Tuberculosis as Revealed by 16S rRNA Pyrosequencing. PLoS ONE 8: E54574.
- Wallace, R., Rooke, J.A., Duthie, C.A., Hyslop, J.J., Ross, D.W., Waterhouse, A., Watson, M., & Roehe, R. (2015) The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 16: 839.
- Casarin. R.C.V., Saito, D., Santos, V.R., Pimentel, S.P., Duarte, M.P., Casati,M.Z., Goncalves (2012) Detection of Mogibacterium timidum in subgingival biofilm of aggressive and non-diabetic and diabetic chronic periodontitis patients. Braz J Microbiol 43: 931-937.
- Durkin, A.S., McCorrison, J., Torralba, M., Gillis, M., Haft, D.H., Methe, B., Sutton, G., & Nelson, K.E. Mogibacterium timidum: ATCC 33093, Whole Genome Sequencing Project. Submitted 16 Jan 2014 by the J Craig Venter Institute, 9704 Medical Centre Dr., Rockville, MD, 20850, USA.
- Al-Ahmad, A., Ameen, H., Pelz, K., Karygianni, L., Wittmer, A>, Anderson A.C., Spitzmuller, B., & Hellwig, E. (2014). Antibiotic Resistance and Capacity for Biofilm Formation of Different Bacteria Isolated from Endodontic Infections Associated with Root-filled Teeth. J Endod 40: 223-230.
- Nakazawa, F., Miyakawa, H., Fujita, M., & Kamaguchi, A. (2011). Significance of Asaccharolytic Eubacterium and Closely Related Bacterial Species in the Human Oral Cavity. J Exp Clin Med 3:17-21.
- Cheeseman, S.L., Hiom, S.J., Weightman, A.J., & Wade, W.G. Phylogeny of Oral Asaccharolytic Eubacterium Species Determined by 16S Ribosomal DNA Sequence Comparison and Proposal of Eubacterium infirmum sp. nov. and Eubacterium tardum sp. nov. Int J Syst Evol Microbiol 46:957-959.
- Sakamoto. M., Rocas, I.N., Siqueira, J.F., & Benno, Y. (2006) Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol <b.21: 112-122.
- Moore, W.E., Holdeman, L.V., Cato, E.P., Smibert, R.M., & Burmeister, J.A. (1983) Bacteriology of moderate (chronic) periodontitis in mature adult humans. Infect Immun 42: 510-515.
- Moore, W.E.C, & Moore, L.V.H. (1994) The bacteria of periodontal diseases. Periodontol 5: 66-77.
- Gomes, B.P.F.A, Berber, V.B, Kokaras, A.S., Chen, T., & Paster, B.J. (2015) Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical preparation. J Endod 41:1975-1984.
- Mayanagi, G., Sato, T., Shimauchi, H., & Takahashi, N. (2004) Detection Frequency of periodontitis-associated bacteria by polymerase chain reaction in subgingival and supragingival plaque of periodontitis and healthy subjects. Oral Microbiol Immunol 19: 379-385.
- Marchesan, J.T., Morelli, T., Moss, K., Barros, S.P., Ward, M., Jenkins, W., Aspiras, M.B., & Offenbacher, S. (2015) Association of Synergistets and Cyclopeptides with Periodontitis. J Dent Res 94: 1425-1431.
- Moore, W.E., Holdeman, L.V., Cato, E.P., Smibert, R.M., Burmeister, J.A., Palcanis, K.G., & Ranney, R.R. (1985) Comparative bacteriology of juvenile. Infect Immun 48: 507-519.
- Smith, A.J., & Wade, W.G., (1999) Serum antibody response against oral Eubacterium species in periodontal disease. J Peridontal Res 34: 175-178.
This page is written by Joshua Monteith for the MICR3004 course, Semester 2, 2017