Streptomycetaceae: Phylogeny, Ecology and Pathogenicity


The family Streptomycetaceae contains three genera, Streptomyces, Kitasatospora and Streptacidiphilus, with Streptomyces being the best known and most diverse of these three genera. Members of this family are adapted to a wide range of environmental conditions and habitats, and show a variety of colony – and cell morphological characteristics. Streptomyces are notable for their complex developmental cycle and production of bioactive secondary metabolites, producing more than two‐thirds of commercially available and clinically useful antibiotics of natural origin (e.g. neomycin, cypemycin, grisemycin, bottromycins and chloramphenicol). Antibacterial, antifungal, antiparasitic and immunosuppressant compounds have all been identified as products of Streptomyces secondary metabolism. Isolated predominantly from soil and decaying vegetation, most streptomycetes produce spores. Many of them produce a distinct ‘earthy’ odour that results from production of a volatile metabolite, geosmin. They are also capable of forming many and diverse hydrolytic exoenzymes, like cellulases and chitinases. The genetics and genomics of streptomycetes is a rapidly developing area. Only a few Streptomyces species are known to be pathogens, although infections, in humans, such as mycetoma, can be caused by S. somaliensis and S. sudanensis, and in plants can be caused by S. caviscabies, S. acidiscabies, S. turgidiscabies and S. scabies.

Key Concepts

  • Comparisons of whole genome sequences will become the future basis of classification of Streptomyces species.
  • Morphological and physiological features as well as chemotaxonomic markers remain distinctive and important for the taxonomy of the family Streptomycetaceae.
  • Genetics and Genomics of streptomycetes reveal complex mechanisms of adaptation to various environments.
  • Antimicrobial compounds and other secondary metabolites are produced in natural habitats inter‐kingdom communication, as signal molecules or defence molecules to defend a growth niche.

Keywords: streptomycetes; phylogeny; taxonomy; life cycle; habitat; antibiotic producers; pathogenicity

Figure 1. Phylogenetic relatedness of the families of the order of Actinomycetales based on 16S rRNA gene sequence comparison. The dendrogram was constructed by analysing approximately 1400 bp of each sequence with the maximum parsimony method contained in the ARB software package. A total of 4032 sequences were analysed. Bar, 0.1% divergence.
Figure 2. Life cycle of streptomycetes grown on solid media. Unlike most bacteria, streptomycetes exhibit a complex multicellular development. (a) Initially, a filamentous mycelium colonises its substrate. After a period of assimilative growth, (b) aerial hyphae grow into the air and eventually (c) septate to form chains of pigmented exospores. Reproduced from Claesen et al. (2006) Regulation of streptomyces developments: reach for the sky! Trends in Microbiology 14(D): 313–319, © Elsevier.
Figure 3. Spore chain morphology of various Streptomyces strains. Morphological features: (a) Rectus‐Flexibilis with warty surface; (b) Rectus‐Flexibilis with hairy surface; (c) Spira with smooth surface; (d) Retinaculum‐Apertum with smooth surface. With the kind permission of Dr. Joachim Wink, Aventis Pharma Deutschland GmbH.
Figure 4. Colour patterns of various Streptomyces strains. (a) Streptomyces spectabilis, (b) S. purpurascens, (c) S. cinereoruber subsp. cinereoruber, (d) S. glaucescens, (e) S. violaceus, (f) S. lateritius.
Figure 5. Streptomyces sp. grow out of a surface sterilised grass root that was put on an agar plate and incubated for several weeks at 25 °C.
Figure 6. Colonies of Streptomyces somaliensis, a human pathogen. With the kind permission of Dr. Joachim Wink, Aventis Pharma Deutschland GmbH.


Abdelmohsen UR, Pimentel‐Elardo SM, Hanora A, et al. (2010) Isolation, phylogenetic analysis and anti‐infective activity screening of marine sponge‐associated actinomycetes. Marine Drugs 8: 399–412.

Abdelmohsen UR, Yang C, Horn H, et al. (2014) Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity. Marine Drugs 12 (5): 2771–2789.

Barbe V, Bouzon M, Mangenot S, et al. (2011) Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. Journal of Bacteriology 193 (18): 5055–5056.

Bentley SD, Chater KF, Cerdeño‐Tárraga AM, et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (6885): 141–147.

Braña AF, Fiedler HP, Nava H, et al. (2015) Two Streptomyces species producing antibiotic, antitumor, and anti‐inflammatory compounds are widespread among intertidal macroalgae and deep‐sea coral reef invertebrates from the central Cantabrian Sea. Microbial Ecology 69 (3): 512–524.

Chen CW, Huang CH, Lee HH, et al. (2002) Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes. Trends in Genetics 18: 522–529.

Colquhoun JA, Heald SC, Li L, et al. (1998) Taxonomy and biotransformation activities of some deep‐sea actinomycetes. Extremophiles 2 (3): 269–277.

Donadio S, Sosio M and Lancini G (2002) Impact of the first Streptomyces genome sequence on the discovery and production of bioactive substances. Applied Microbiology and Biotechnology 60: 377–380.

Dyson P (2010) Streptomyces: Molecular Biology and Biotechnology. Norwich, UK: Caister Acad Press.

Guo Y, Zheng W, Rong X, et al. (2008) A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. International Journal of Systematic and Evolutionary Microbiology 58: 149–159.

Gevers D, Cohan FM, Lawrence JG, et al. (2005) Re‐evaluating prokaryotic species. Nature Reviews Microbiology 3: 733–739.

Gravius B, Glocker D, Pigac J, et al. (1994) The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome. Microbiology 140: 2271–2277.

Han JH, Cho MH and Kim SB (2012) Ribosomal and protein coding gene based multigene phylogeny on the family Streptomycetaceae. Systematic and Applied Microbiology 35: 1–6.

Hsiao N‐H and Kirby R (2008) Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system. Antonie van Leeuwenhoek 93: 1–25.

Hopwood DA (1999) Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico. Microbiology 145 (Pt 9): 2183–2202.

Hopwood DA (2007) Streptomyces in Nature and Medicine: The Antibiotic Makers. New York: Oxford University Press.

Ian E, Malko DB, Sekurova ON, et al. (2014) Genomics of sponge‐associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential. PLoS One 9 (5): e96719.

Ikeda H, Ishikawa J and Hanamoto A (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotechnology 21 (5): 526–531.

Jog R, Pandya M, Nareshkumar G, et al. (2014) Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth. Microbiology 160: 778–788.

Kieser T, Bibb MJ, Buttner MJ, et al. (2000a) Practical Streptomyces Genetics. Norwich, U.K.: The John Innes Foundation.

Kinashi H, Shimaji‐Murayama M and Hanafusa T (1991) Nucleotide sequence analysis of the unusually long terminal inverted repeats of a giant linear plasmid, SCP1. Plasmid 26: 123–130.

Korn‐Wendisch F and Kutzner HJ (1992) The family Streptomycetaceae. In: Balows A, Trüper HG, Dworkin M, Harder W and Schleifer KH (eds) The Prokaryotes, pp. 921–995. New York: Springer.

Lehr NA, Schrey SD, Hampp R, et al. (2008) Root inoculation with a forest soil streptomycete leads to locally and systemically increased resistance against phytopathogens in Norway spruce. New Phytologist 177: 965–976.

Lonsdale J, Seong CN and Goodfellow M (2003) Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici 1943AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek 83: 107–116.

Ohnishi Y, Ishikawa J and Hara H (2008) Genome sequence of the streptomycin‐producing microorganism Streptomyces griseus IFO 13350. Journal of Bacteriology 190 (11): 4050–4060.

Paradkar A, Trefzer A, Chakraburtty A, et al. (2003) Streptomyces genetics: a genomic perspective. Critical Reviews in Biotechnology 23: 1–27.

Porter JN and Wilhelm JJ (1961) The effect on Streptomyces populations of adding various supplements to soil samples. Developments in Industrial Microbiology 2: 253–259.

Ravel J, Schrempf H and Hill RT (1998) Mercury resistance is encoded by transferable giant linear plasmids in two Chesapeake Bay Streptomyces strains. Applied and Environmental Microbiology 64: 3383–3388.

Rong X, Guo Y and Huang Y (2009) Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA‐DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Systematic and Applied Microbiology 32 (5): 314–322.

Rong X and Huang Y (2010) Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA‐DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. International Journal of Systematic and Evolutionary Microbiology 60 (3): 696–703.

Rong X and Huang Y (2012) Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA‐DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Systematic and Applied Microbiology 35 (1): 7–18.

Rong X and Huang Y (2014) Chapter 11 – Multi‐locus sequence analysis: taking prokaryotic systematics to the next level. In: Goodfellow M, Sutcliffe I and Chun J (eds) Methods in Microbiology, vol. 41, pp. 221–251. Academic Press.

Salla TD, da Silva R, Astarita LV, et al. (2014) Streptomyces rhizobacteria modulate the secondary metabolism of Eucalyptus plants. Plant Physiology and Biochemistry 85: 14–20.

Schrempf H (2006) The family Streptomycetaceae ‐ Part II: Molecular Biology. In: Dworkin M et al. (eds) The Prokaryotes, vol. 3: Bacteria: Firmicutes, Actinomycetes, pp. 605–622. New York: Springer‐Verlag.

Ventura M, Canchaya C and Tauch A (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiology and Molecular Biology Reviews 71: 495–548.

Vogelmann J, Ammelburg M, Finger C, et al. (2011) Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation by FtsK/SpoIIIE. EMBO Journal 30 (11): 2246–2254.

Waksman SA and Henrici AT (1943) The nomenclature and classification of the actinomycetes. Journal of Bacteriology 46: 337–341.

Wang XJ, Yan YJ, Zhang B, et al. (2010) Genome sequence of the milbemycin‐producing bacterium Streptomyces bingchenggensis. Journal of Bacteriology 192 (17): 4526–4527.

Warcup JH (1950) The soil‐plate method for isolation of fungi from soil. Nature 166: 117–118.

Zhang Z, Wang Y and Ruan J (1997) A proposal to revive the genus Kitastospora (Ōmura, Takahashi, Iwai, and Tanaka 1982). International Journal of Systematic Bacteriology 47: 1048–1054.

Further Reading

Kämpfer P (2006) The family Streptomycetaceae – Part 1: taxonomy. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K‐H and Stackebrandt E (eds) The Prokaryotes, vol. 3, pp. 538–604. New York: Springer.

Kämpfer P, Glaeser SP, Parkes L, van Keulen G and Dyson P (2014) The family Streptomycetaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E and Thompson F (eds) The Prokaryotes, 4th – Actinobacteria edn, pp. 889–1010. Berlin, Heidelberg: Springer‐Verlag.

Kieser T, Bibb MJ, Buttner MJ, Chater KF and Hopwood DA (2000b) Practical Streptomyces Genetics. Norwich: The John Innes Foundation.

Miyadoh S, Tsuchizaki N, Ishikawa J and Hotta K (2015) Digital Atlas of Actinomycetes. (accessed 14 Nov 2015).

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Glaeser, Stefanie P, and Kämpfer, Peter(Jan 2016) Streptomycetaceae: Phylogeny, Ecology and Pathogenicity. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020392.pub2]