Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 11;8(1):525.
doi: 10.1038/s41598-017-17392-0.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

Lorena Carro  1 , Imen Nouioui  2 , Vartul Sangal  3 , Jan P Meier-Kolthoff  4 , Martha E Trujillo  5 , Maria Del Carmen Montero-Calasanz  2 , Nevzat Sahin  6 , Darren Lee Smith  3 , Kristi E Kim  7 , Paul Peluso  7 , Shweta Deshpande  8 , Tanja Woyke  8 , Nicole Shapiro  8 , Nikos C Kyrpides  8 , Hans-Peter Klenk  9 , Markus Göker  4 , Michael Goodfellow  2
Affiliations

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

Lorena Carro et al. Sci Rep. .

Abstract

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Micromonospora phylogeny inferred using the Genome BLAST Distance Phylogeny (GBDP) approach. The tree was inferred using the FastME from the GBDP intergenomic distances calculated from whole proteomes. The numbers above branches are GBDP pseudo-bootstrap support values from a 100 replicates, only values above 50% are shown. Tip colours on the right indicate the habitats from which the strains were isolated, those in the middle-right indicate genomic DNA G+C content, as embedded in the legends. Tip colours on the left indicate selected clades within the genus and those on the middle-left indicate well-supported subgroups within this clades.
Figure 2
Figure 2
Tip permutation test analysis of Micromonospora features respect to phylogenomics. Shown are the p-values from the tests of individual characters arranged by kind of character. The dotted lines represent alpha levels (0.01, 0.05, 0.10). With exceptions for some fatty acids, no correlation was observed between phenotypic data (C source: carbon sources; chemotaxonomy: other than fatty acid data; enzyme production; fatty acids; and growth at several temperatures, pH and percentage of salinity) and genome scale phylogeny. The single genes (16S rRNA, atpD, gyrB, recA, rpoB) presented few significant phylogenetically conserved characters. The number of BCs (biosynthetic gene clusters) classified by type of organic compounds presented no detectable phylogeny conservation, whereas some COGs categories and the GC content (as part of the group of other genomic characters) were significantly conserved.
Figure 3
Figure 3
Principal coordinate analysis of topological distances. The analysis of the bootstrap-weighted relative Robinson-Foulds topological distances as calculated by RAxML shows that the lowest distances were between the whole genome sequence phylogeny (GBDP) and the MLSA phylogenies and the highest ones between the 16S rRNA gene phylogenies (SSU) and the GBDP tree; the distances with the other individual trees lay within these ranges. ML, maximum likelihood; MP, maximum parsimony; PB, partition bootstrap.
Figure 4
Figure 4
Biosynthetic gene clusters found in the Micromonospora genomes using antiSMASH 3.0. Highly variable profiles were found between the strains. The genomes of the Micromonospora strains were found to be especially rich in NRPS, PKS and terpene clusters; whereas there was also an abundance of bacteriocin, lantipeptide and siderophores clusters.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Priest, F. & Goodfellow, M. (Eds) Applied Microbial Systematics. (Kluwer Academic Publishers, 2000).
    1. Goodfellow, M., Sutcliffe, I. C. & Chun, J. (Eds) New Approaches to Prokaryotic Systematics. (Academic Press, 2014).
    1. Goodfellow, M. & O’Donnell, A. G. (Eds) New Bacterial Systematics. (Academic Press, 1993).
    1. Goodfellow M, Freeman R, Sisson PR. Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology. Zentralbl Bakteriol. 1997;285:133–156. doi: 10.1016/S0934-8840(97)80023-0. - DOI - PubMed
    1. Colwell RR. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol. 1970;104:410–433. - PMC - PubMed

Publication types

LinkOut - more resources

-