Several nocardioform actinomycetes were isolated from tufaceous surfaces with whitish-grey patinas in the catacombs of St Callistus in Rome, Italy. The morphology of the isolates and their chemotaxonomic characteristics such as -diaminopimelic acid in the cell-wall peptidoglycan, the major menaquinone of MK-9(H), phosphatidylinositol, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids, as well as complex cellular fatty acid patterns with anteiso-C, iso-C and iso-C as predominating components, were in agreement with their classification as members of the genus by 16S rRNA gene sequence analysis. The isolates fell into two clusters as revealed by their ribosomal intergenic spacer, RiboPrint and cellular fatty acid patterns and by their MALDI-TOF mass spectra. The two clusters were represented by the strains BC631 and BC633 which shared 97.9 % 16S rRNA gene sequence similarity. Strain BC631 represented a cluster of yellow pigmented strains and was a phylogenetic neighbour of DSM 17837 (gene sequence similarity 98.0 %), while strain BC633 was related to DSM 17836 and DSM 17344 (gene sequence similarities of 98.8 % and 98.6 %, respectively). Strains BC631 and BC633 could be differentiated from each other and from their closest phylogenetic neighbours by phenotypic characteristics and DNA–DNA relatedness values far below 70 %. It is concluded that the two new strains represent two novel species, for which the names sp. nov. (type strain BC631=DSM 19601=JCM 14968) and sp. nov. (type strain BC633=DSM 19602=JCM 14969) are proposed.


Article metrics loading...

Loading full text...

Full text loading...



  1. Anderson, J. A.(1939). The use of tributyrin agar in dairy bacteriology. Ber 3 Int Mikrobiol Kongress 3, 726–728. [Google Scholar]
  2. Bauer, A. W., Kirby, W. M., Sherris, J. C. & Turck, M.(1966). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45, 493–496. [Google Scholar]
  3. Borin, S., Daffonchio, D. & Sorlini, C.(1997). Single strand conformation polymorphism analysis of PCR-tDNA fingerprinting to address the identification of Bacillus species. FEMS Microbiol Lett 157, 87–93.[CrossRef] [Google Scholar]
  4. Bruce, J.(1996). Automated system rapidly identifies and characterizes microorganisms in food. Food Technol 50, 77–81. [Google Scholar]
  5. Carlsohn, M. R., Groth, I., Spröer, C., Schütze, B., Saluz, H.-P., Munder, T. & Stackebrandt, E.(2007).Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57, 1943–1947.[CrossRef] [Google Scholar]
  6. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M.(1977). A rapid method for base ratio determination of bacterial DNA. Anal Biochem 81, 461–466.[CrossRef] [Google Scholar]
  7. Collins, M. D., Pirouz, T. & Goodfellow, M.(1977). Distribution of menaquinones in actynomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef] [Google Scholar]
  8. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurements of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  9. Everest, G. J. & Meyers, P. R.(2008).Kribbella hippodromi sp. nov. isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 58, 443–446.[CrossRef] [Google Scholar]
  10. Felsenstein, J.(1993).phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  11. Groth, I. & Saiz-Jimenez, C.(1999). Actinomycetes in hypogean environments. Geomicrobiol J 16, 1–8.[CrossRef] [Google Scholar]
  12. Groth, I., Schumann, P., Weiss, N., Martin, K. & Rainey, F. A.(1996).Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46, 234–239.[CrossRef] [Google Scholar]
  13. Groth, I., Schumann, P., Schuetze, B., Gonzales, J. M., Laiz, L., Saiz-Jimenez, C. & Stackebrandt, E.(2005).Isoptericola hypogeus sp. nov., isolated from the Roman catacomb of Domitilla. Int J Syst Evol Microbiol 55, 1715–1719.[CrossRef] [Google Scholar]
  14. Groth, I., Schumann, P., Schutze, B., Gonzales, J. M., Laiz, L., Suihko, M.-L. & Stackebrandt, E.(2006).Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 56, 283–287.[CrossRef] [Google Scholar]
  15. Gürtler, V.(1993). Typing of Clostridium difficile strains by PCR-amplification of variable length 16S–23S rDNA spacer regions. J Gen Microbiol 139, 3089–3097.[CrossRef] [Google Scholar]
  16. Gürtler, V. & Stanisich, V. A.(1996). New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer region. Microbiology 142, 3–16.[CrossRef] [Google Scholar]
  17. Huß, V. A. R., Festl, H. & Schleifer, K. H.(1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef] [Google Scholar]
  18. Jurado, V., Groth, I., Gonzalez, J. M., Laiz, L., Schuetze, B. & Saiz-Jimenez, C.(2005a).Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 55, 871–875.[CrossRef] [Google Scholar]
  19. Jurado, V., Laiz, L., Gonzalez, J. M., Hernandez-Marine, M., Valens, M. & Saiz-Jimenez, C.(2005b).Phyllobacterium catacumbae sp. nov., a member of the order ‘Rhizobiales’ isolated from Roman catacombs. Int J Syst Evol Microbiol 55, 1487–1490.[CrossRef] [Google Scholar]
  20. Kirby, B. M., Le Roes, M. & Meyers, P. R.(2006).Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from the Western Cape, South Africa. Int J Syst Evol Microbiol 56, 1097–1101.[CrossRef] [Google Scholar]
  21. Lee, S. D., Kang, S.-O. & Hah, Y. C.(2000).Hongia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 50, 191–199.[CrossRef] [Google Scholar]
  22. Li, W.-J., Wang, D., Zhang, Y.-Q., Schumann, P., Stackebrandt, E., Xu, L.-H. & Jiang, C.-L.(2004).Kribbella antibiotica sp. nov., a novel nocardioform actinomycete strain isolated from soil in Yunnan, China. Syst Appl Microbiol 27, 160–165.[CrossRef] [Google Scholar]
  23. Li, W.-J., Wang, D., Zhang, Y.-Q., Xu, L.-H. & Jiang, C.-L.(2006).Kribbella yunnanensis sp. nov., Kribbella alba sp. nov., two novel species of genus Kribbella isolated from soils in Yunnan, China. Syst Appl Microbiol 29, 29–35.[CrossRef] [Google Scholar]
  24. Luedemann, G. M.(1968).Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96, 1848–1858. [Google Scholar]
  25. Minnikin, D. E., Collins, M. D. & Goodfellow, M.(1979). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47, 87–95.[CrossRef] [Google Scholar]
  26. Park, Y. H., Yoon, J. H., Shin, Y. K., Suzuki, K., Kudo, T., Seino, A., Kim, H. J., Lee, J. S. & Lee, S. T.(1999). Classification of “Nocardioides fulvus” IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49, 743–752.[CrossRef] [Google Scholar]
  27. Pridham, T. G. & Gottlieb, D.(1948). The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 56, 107–114. [Google Scholar]
  28. Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt, E.(1996). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46, 1088–1092.[CrossRef] [Google Scholar]
  29. Rhuland, L. E., Work, E., Denman, R. F. & Hoare, D. S.(1955). The behavior of the isomers of α,ϵ-diaminopimelic acid on paper chromatograms. J Am Chem Soc 77, 4844–4846.[CrossRef] [Google Scholar]
  30. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  31. Schwieger, F. & Tebbe, C. C.(1998). A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64, 4870–4876. [Google Scholar]
  32. Shirling, E. B. & Gottlieb, D.(1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef] [Google Scholar]
  33. Sierra, G.(1957). A simple method for the detection of lipolytic activity of microorganisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 23, 15–22.[CrossRef] [Google Scholar]
  34. Sneath, P. H., Mair, N. S., Sharpe, M. E. & Holt, J. G.(1986).Bergey's Manual of Systematic Bacteriology, vol. 2. Baltimore: Williams & Wilkins.
  35. Sohn, K., Hong, S. G., Bae, K. S. & Chun, J.(2003). Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 53, 1005–1007.[CrossRef] [Google Scholar]
  36. Song, J., Kim, B.-Y., Hong, S.-B., Cho, H.-S., Sohn, K., Chun, J. & Suh, J. W.(2004).Kribbella solani sp. nov. and Kribbella jejuensis sp. nov., isolated from potato tuber and soil in Jeju, Korea. Int J Syst Evol Microbiol 54, 1345–1348.[CrossRef] [Google Scholar]
  37. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L.(1997). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479–491.[CrossRef] [Google Scholar]
  38. Stackebrandt, E., Breymann, S., Steiner, U., Prauser, H., Weiss, N. & Schumann, P.(2002). Re-evaluation of the status of the genus Oerskovia, reclassification of Promicromonospora enterophila (Jáger et al. 1983) as Oerskovia enterophila comb. nov. and description of Oerskovia jenensis sp. nov. and Oerskovia paurometabola sp. nov. Int J Syst Evol Microbiol 52, 1105–1111.[CrossRef] [Google Scholar]
  39. Stead, D. E., Sellwood, J. E., Wilson, J. & Viney, I.(1992). Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. J Appl Bacteriol 72, 315–321.[CrossRef] [Google Scholar]
  40. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  41. Tiecco, G.(1975).Microbiologia Degli Alimenti Di Origine Animale. Bologna: Edizioni Agricole.
  42. Trujillo, M. E., Kroppenstedt, R. M., Schumann, P. & Martinez-Molina, E.(2006).Kribbella lupini sp. nov. isolated from the roots of Lupinus angustifolius. Int J Syst Evol Microbiol 56, 407–411.[CrossRef] [Google Scholar]
  43. Urzì, C., Brusetti, L., Salamone, P., Sorlini, C., Stackebrandt, E. & Daffonchio, D.(2001). Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. Environ Microbiol 3, 471–479.[CrossRef] [Google Scholar]
  44. Urzì, C., De Leo, F., Donato, P. & La Cono, V.(2003). Multiple approach to study the structure and diversity of microbial communities colonizing artistic surfaces. Study case: the Roman Catacombs of St Callistus and Domitilla. In Molecular Biology and Cultural Heritage, pp. 187–193. Edited by C. Saiz-Jimenez. Lisse: Swets & Zeitlinger.
  45. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef] [Google Scholar]
  46. Williams, S. T., Goodfellow, M. & Alderson, G.(1989). Genus Streptomyces. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2452–2492. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  47. Williams, S. T., Goodfellow, M., Alderson, G., Wellington, E. M. H., Sneath, P. H. A. & Sackin, M. J.(1983). Numerical classification of Streptomyces and related genera. J Gen Microbiol 129, 1743–1813. [Google Scholar]

Data & Media loading...


vol. , part 9, pp. 2090 - 2097

SEM observation of strains.

Euclidian distance dendrogram generated by the software of the Sherlock Microbial Identification System based on fatty acid profiles of , and of the phylogenetically related type strains DSM 17836 , DSM 17344 and DSM 17837 .

Electrophoretic gel on 2% agarose of ITS (internal transcribed spacer) PCR products of strains of the genus .

Diversity of normalized PvuII RiboPrint patterns found within strains of , and type strains of the phylogenetically related species , and .

Dendrogram generated by the BioTyper software (version 1.1, Bruker Daltonics) showing the similarity of MALDI-TOF mass spectra of cell extracts of strains of , and of the type strains of the phylogenetically related species , and .

Combined file [ PDF] 658 KB

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error