Standards in Genomic Sciences (2013) 9:395-409 DOI:10.4056/sig s.4628316 Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Ajay Kumar Mishra1, Jean-Christophe Lagier1, Anne Pfleiderer1, Thi Thien Nguyen1, Aurelia Caputo1, Didier Raou lt1,2 and Pierre-Edouard Fournier1* 1URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France* 2King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia *Correspondence: Pierre-Edouard Fournier ([email protected]) Keywords: Holdemania massiliensis, genome, culturomics, taxono-g enomics. Hol deman ia mass il ie ns is st rain AP2T sp. nov. is the type strain of H. mass il iens is sp. nov., a new species within the genus Holdemania. This strain, whose g enome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massil iens is is a Gram-positive, anaerobic bacillus. Here we describe the features of this org anism, tog ether with the complete genome sequence and an- notation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA g enes. Introduction Holdemania massiliensis strain AP2T (= CSUR P195 The genus Holdemania (Willems et al. 1997) was = DSM 26143) is the type strain of H. massiliensis created in 1997 on the basis of 16S rDNA gene se- sp. nov. This bacterium is a Gram-positive, non- quence, biochemical tests, fatty acid and cell wall spore-forming, indole negative, anaerobic and murein analysis [28]. To date, this genus includes non-motile bacillus that was isolated from the a single species, H. filiformis, which was isolated stool of a 21-year-old woman suffering from ano- from feces of healthy humans [29]. rexia as part of a “culturomics” study aiming to individually cultivate all species within human Classification and features feces [1-3]. A stool sample was collected from a 21-year-old The current prokaryotic species classification, French Caucasian female suffering from severe known as polyphasic taxonomy, is based on a restrictive anorexia nervosa, who had been hospi- combination of genomic and phenotypic proper- talized for recurrent weight loss and aggravation ties [4]. The number of sequenced genomes is in- of her general state. She had an eight year history creasing exponentially and in parallel with the de- of mental anorexia. The patient gave an informed creasing cost of sequencing. To date, more than and signed consent. Both this study and the assent 6,000 bacterial genomes have been published and procedure were approved by the Ethics Commit- approximately 25,000 genomes project are antici- tee of the Institut Fédératif de Recherche IFR48, pated to be completed in a near future [5]. We re- Faculty of Medicine, Marseille, France and the cently proposed to integrate genomic information agreement of the ethics committee of the IFR48 in the taxonomic framework and description of (Marseille, France) was obtained under reference new bacterial species [6-27]. 09-022. Several other new bacterial species were Here we present a summary classification and a isolated from diverse stool samples using micro- set of features for H. massiliensis sp. nov. strain bial culturomics [6-27]. The fecal specimen from AP2T (= CSUR P195 = DSM 26143), together with the patient was preserved at -80°C immediately the description of the complete genomic sequenc- after collection. Strain AP2T (Table 1) was isolated ing and annotation. These characteristics support in November 2011 after preincubation in an an- the circumscription of the species H. massiliensis. aerobic blood culture bottle with the addition of The Genomic Standards Consortium Holdemania massiliensis sp. nov. 5ml of thioglycolate, and inoculation in Columbia [29] (Figure 1). This value was lower than the agar (BioMerieux, Marcy l’Etoile, France). 98.7% 16S rRNA gene sequence threshold rec- This strain exhibited a 97% nucleotide sequence ommended by Stackebrandt and Ebers to deline- similarity with H. filiformis [28], and a range of 90- ate a new species without carrying out DNA-DNA 91% nucleotide sequence similarity to most close- hybridization [40]. ly related members of the genus Erysipelothrix Table 1. Classification and general features of Holdemania massiliensis strain AP2T according to the MIGS recommendations [30] MIGS ID Property Term Evidence codea Domain Bacteria TAS [31] Phylum Firmicutes TAS [32 -34 ] Class Erysipelotrichia TAS [35,36] Current classification Order Erysipelotrichales TAS [36,37] Family Erysipelotrichaceae TAS [38] Genus Holdemania TAS [28] Species Holdemania massiliensis IDA T Type strain AP2 IDA Gram stain positive IDA Cell shape Bacillus IDA Motility Not motile IDA Sporulation Non-sporulating IDA Temperature range Mesophile IDA Optimum temperature 37°C IDA MIGS-6.3 Salinity Unknown IDA MIGS-22 Oxygen requirement Anaerobic IDA Carbon source Unknown NAS Energ y source Unknown NAS MIGS-6 Habitat Human g ut IDA MIGS-15 Biotic relationship Free living IDA MIGS-14 Pathogenicity Unknown NAS Biosafety level 2 Isolation Human feces MIGS-4 Geog raphic location France IDA MIGS-5 Sample collection time November 2011 IDA MIGS-4.1 Latitude 43.296482 IDA MIGS-4.1 Long itude 5.36978 IDA MIGS-4.3 Depth Surface IDA MIGS-4.4 Altitude 0 m above sea level IDA Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). The- se evidence codes are from the Gene Ontology project [39]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledge- ments. 396 Standards in Genomic Sciences Mishra et al. Figure 1. Phylogenetic tree highlig hting the position of Holdemania massiliensis strain AP2T relative to other type strains within the Erysipelotrichaceae family. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtaine d using the max imum-likelihood method within MEGA program. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Eggerthella lenta was use d as outg roup . The sca le ba r rep rese nts a 2% nucleotide sequence divergence. Different growth temperatures (25, 30, 37, 45°C) GENbag anaer and GENbag microaer systems, re- were tested. Growth occurred at 25 and 30°C after spectively (BioMérieux), and under aerobic condi- 72 hours of inoculation and the optimal growth tions with or without 5% CO2. The strain growth was observed at 37°C after 24 hours of inocula- was obtained only in anaerobic condition. The mo- tion. Colonies were 0.2 mm in diameter, light grey, tility test was negative. Cells grown on agar are -haemolysis on blood-enriched Columbia Gram-positive rods (Figure 2). The mean dimen- agar. Growth of the strain was tested under an- sions by electron microscopy were 0.57 µm in aerobicwith α and microaerophilic conditions using width and 1.75 µm in length (Figure 3). Figure 2. Gram staining of H. massil iens is strain AP2T http://standardsing enomics.org 397 Holdemania massiliensis sp. nov. Figure 3. Transmission electron microscopy of H. massiliensis strain AP2T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm. Strain AP2T exhibited a positive oxidase but no carried out as previously described [41] using a catalase activity. Using an API rapid 32A strip Microflex spectrometer (Bruker Daltonics, Leipzig, (Biomerieux), positive reactions were obtained for Germany). Twelve individual colonies were depos- -gala - -fucosidase and ited on a MTP 384 MALDI-TOF target plate pyroglutamic acid arylamidase. Substrate oxida- (Bruker). The twelve AP2T spectra were imported tionβ andctosidase, assimilation α glucosidase, was examined α using an API into the MALDI BioTyper software (version 2.0, 50CH strip (Biomerieux) at 37°C. Positive reac- Bruker) and analyzed by standard pattern match- tions were observed for glycerol, D-ribose, D- ing (with default parameter settings) against the galactose, D-glucose, D-fructose, D-mannose, ino- main spectra of 4,706 bacteria. A score enabled sitol, D-mannitol, D-sorbitol, N-acetyl- the presumptive identification and discrimination glucosamine, amygdalin, arbutin, esculin, salicin, of the tested species from those in a database: a D-cellobiose, D-maltose, D-lactose, D-saccharose, score > 2 with a validated species enabled the D-melezitose, gentiobiose, D-tagatose and identification at the species level; and a score < 1.7 postassium gluconate. H. massiliensis is suscepti- did not enable any identification. For strain AP2T, ble to amoxicillin, metronidazole, vancomycin, no significant score was obtained, suggesting that clindamycin and imipenem. The phenotypic char- our isolate was not a member of any known spe- acteristics that differentiate H. massiliensis from cies (Figures 4 and 5). We added the spectrum other species are summarized in Table 2. from strain AP2T to our database (Figure 4). Matrix-assisted laser-desorption/ionization time- of-flight (MALDI-TOF) MS protein analysis was 398 Standards in Genomic Sciences Mishra et al. Table 2. Differential characteristics