Abstract
We report the main properties of “Actinomyces ihumii” strain SD1 (= CSUR P2006) isolated from the stool of a 50-year-old HIV-infected man.
Keywords: Actinomyces ihumii, culturomics, emerging bacteria, gut microbiota, taxonomy
In April 2015, we cultivated a stool specimen from a 50-year-old HIV-infected male patient. The patient was asymptomatic at the time of sampling. We isolated a strain in pure culture, strain SD1, for which matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using a MicroFlex spectrometer (Bruker Daltonics, Leipzig, Germany) failed to provide any reliable identification (score <1.7) [1]. The stool sample was cultivated as part of a culturomics study of the human microbiome [2]. The patient provided signed informed consent. Approval of the study by the local ethics committee of IFR48 (Marseille, France) was obtained under agreement number 09-022.
Strain SD1 was initially obtained in microaerophilic atmosphere on 5% sheep's blood–enriched Columbia agar (bioMérieux, Marcy l'Etoile, France) after 48 hours of incubation at 37°C. Colonies were bright grey with a diameter of 1 to 2 mm on blood-enriched agar (bioMérieux). Bacterial cells were not motile, and non-spore-forming Gram-positive rod-shaped bacilli had a diameter of 0.5 to 0.7 μm and a length of 0.7 to 1 μm. Strain SD1 exhibited no catalase or oxidase activity. The complete 16S rRNA gene was sequenced using the fD1-rP2 primers as previously described [3], using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain SD1 exhibited a 98.6 % 16S rRNA gene sequence identity with Actinomyces radingae strain APL1T (GenBank accession no. NR026169), the phylogenetically closest species with standing in nomenclature (Fig. 1) [4]. A. radingae is a facultative anaerobic Gram-positive rod isolated from mixed cultures from various infectious processes. It exhibits no catalase and oxidase activity, and colonies on sheep's blood-enriched agar are whitish to greyish, and about 0.3 to 0.5 mm in diameter.
Fig. 1.
Phylogenetic tree showing position of Actinomyces ihumii strain SD1T relative to other phylogenetically close members of genus Actinomyces. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences were obtained using maximum-likelihood method within MEGA software. Numbers at nodes are percentages of bootstrap values obtained by repeating analysis 500 times to generate majority consensus tree. Only values greater than 95% were displayed. Arcanobacterium phocae was used as outgroup. Scale bar = 1% nucleotide sequence divergence.
Because strain SD1T exhibited a 16S rRNA gene sequence identity of <98.65% with its phylogenetically closest species with a validly published name [5], we propose that it may be a representative strain of a new species within the genus Actinomyces. Consequently, we formally propose the creation of the new species “Actinomyces ihumii” sp. nov. (i.hum.i'i. N.L. gen. n. ihumii, based on the acronym IHUMI, for Institut Hospitalo-Universitaire Méditerranée-Infection in Marseille, France, where the type strain was isolated), with strain SD1T as the type strain.
MALDI-TOF-MS spectrum accession number
The MALDI-TOF-MS spectrum of A. ihumii is available online (http://www.mediterraneeinfection.com/article.php?laref=256&titre=urms-database).
Nucleotide sequence accession number
The 16S rRNA gene sequence was deposited in GenBank under accession number LN866997.
Deposit in a culture collection
Strain SD1T was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR) under number P2006.
Acknowledgement
This study was funded by the Fondation Méditerranée Infection.
Conflict of Interest
None declared.
References
- 1.Seng P., Abat C., Rolain J.M., Colson P., Lagier J.C., Gouriet F. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol. 2013;51:2182–2194. doi: 10.1128/JCM.00492-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Lagier J.C., Hugon P., Khelaifia S., Fournier P.E., La Scola B., Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev. 2015;28:237–264. doi: 10.1128/CMR.00014-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Drancourt M., Bollet C., Carlioz A., Martelin R., Gayral J.P., Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol. 2000;38:3623–3630. doi: 10.1128/jcm.38.10.3623-3630.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Wüst J., Stubbs S., Weiss N., Funke G., Collins M.D. Assignment of Actinomyces pyogenes–like (CDC coryneform group E) bacteria to the genus Actinomyces as Actinomyces radingae sp. nov. and Actinomyces turicensis sp. nov. Lett Appl Microbiol. 1995;E20:76–81. doi: 10.1111/j.1472-765x.1995.tb01290.x. [DOI] [PubMed] [Google Scholar]
- 5.Kim M., Oh H.S., Park S.C., Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–351. doi: 10.1099/ijs.0.059774-0. [DOI] [PubMed] [Google Scholar]