Nisha B. Patel

Propionibacterium namnetense sp. nov., isolated from a human bone infection

A polyphasic taxonomic study was performed on two Gram-positive-staining, anaerobic, pleomorphic, rod-shaped strains isolated from human bone and tissue samples. Sequencing of the 16S rRNA genes revealed that the strains belong to a novel species within the genus Propionibacterium, most closely related to Propionibacterium acnes subsp. acnes and Propionibacterium acnes subsp. elongatum with similarity values of 98.4 % and 98.1 %, respectively. In addition, protein-coding genes for rpoB, recA and gyrB clearly separated the novel organism from all species and subspecies of the genus Propionibacterium. However, a DNA-DNA hybridization analysis between the novel organism and the type strain P. acnes ATCC 6919T revealed a value of only 61.1 %. Furthermore, whole genome analysis using the program OrthoANI gave a value of 88.5 %, which is significantly below the cut-off value of 95 % for species delineation. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The DNA G+C content of the type strain was 59.7 mol%. When taken collectively, phenotypic, molecular genetic, chemotaxonomic and phylogenetic information demonstrate that the organism represents a distinct, albeit close relative of P. acnes On the basis of the results presented, the organism represents a novel member of the genus Propionibacterium for which the name Propionibacterium namnetense sp. nov. is proposed. The type strain is NTS 31307302T (=DSM 29427T=CCUG 66358T).

Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses.

Gram-stain-positive, partially acid-fast, non-spore-forming, anaerobic, catalase-positive, pleomorphic bacteria were isolated from human abscesses. Strains X1036T, X1698 and NML 120705, were recovered from a spinal abscess, a peritoneal abscess and a breast abscess respectively. A phylogenetic analysis of the 16S rRNA gene sequences showed that the strains shared 100 % similarity, and the nearest phylogenetic neighbour was Dietzia timorensis DSM 45568T (95%). Chemotaxonomic characteristics of the strains were consistent with those described for members of the suborder Corynebacterineae. Mycolic acids were detected using HPLC and one-dimensional TLC; whole-cell hydrolysates yielded meso-diaminopimelic acid with arabinose and galactose as the predominant sugars; the muramic acid acyl type was acetylated; the major menaquinone was MK-9 (96.3%); polar lipids detected were phosphatidylglycerol, phosphatidylinositol and an unknown glycophospholipid. Cellular fatty acids were hexadecanoic acid (C16 : 0), octadecenoic acid (C18 : 1ω9c) and decanoic acid (C10 : 0). Tuberculostearic acid was not detected. Based on the results of this polyphasic study, we conclude that these strains represent a novel genus and species within the suborder Corynebacterineae for which we propose the name Lawsonella clevelandensis gen. nov., sp. nov., with the type strain X1036T (=DSM 45743T=CCUG 66657T).

Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere

A Gram-stain-positive bacterium, strain LZ-22T, was isolated from a rhizosphere of moss Leptobryum sp. collected at the shore of Lake Zub in Antarctica. Cells were motile, straight or pleomorphic rods with sizes of 0.6-1.0×3.5-10 µm. The novel isolate was a facultatively anaerobic, catalase-positive, psychrotolerant mesophile. Growth was observed at 3-41 °C (optimum 24-28 °C), with 0-7 % (w/v) NaCl (optimum 0.25 %) and at pH 4.0-9.0 (optimum pH 7.8). The quinone system of strain LZ-22T possessed predominately menaquinone MK-9(H4). The genomic G+C content was 70.2 mol%. Strain 10J was isolated from a biofilm of sediment microbial fuel cell, in Uruguay and had 99 % 16S rRNA gene sequence similarity to strain LZ-22T. DNA-DNA-hybridization values of 84 % confirmed that both strains belonged to the same species. Both strains grew on sugars, proteinaceous compounds, and some amino- and organic acids. Strain LZ-22T uniquely grew on D-enantiomers of histidine and valine while neglecting growth on L-enantiomers. Both strains were sensitive to most of the tested antibiotics but resistant to tested nitrofurans and sulfanilamides. Phylogenetic analyses of the 16S rRNA gene sequences indicated that the strains were related to members of the family Propionibacteriaceae (~93-94 % 16S rRNA gene sequence similarity) with formation of a separate branch within the radiation of the genera Granulicoccus and Luteococcus. Based on phenotypic and genotypic characteristics, we propose the affiliation of both strains into a novel species of a new genus. The name Raineyella antarctica gen. nov., sp. nov. is proposed for the novel taxon with the type strain LZ-22T (=ATCC TSD-18T=DSM 100494T=JCM 30886T).

Non-toxin-producing Bacillus cereus strains belonging to the B. anthracis clade isolated from the international space station

The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions. ABSTRACT In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization–time of flight profiles were consistent with the B. cereus sensu lato group. The phenotypic traits such as motile rods, enterotoxin production, lack of capsule, and resistance to gamma phage/penicillin observed in ISS isolates were not characteristics of B. anthracis. Whole-genome sequence characterizations showed that ISS strains had the plcR non-B. anthracis ancestral “C” allele and lacked anthrax toxin-encoding plasmids pXO1 and pXO2, excluding their identification as B. anthracis. The genetic identities of all 11 ISS isolates characterized via gyrB analyses arbitrarily identified them as members of the B. cereus group, but traditional DNA-DNA hybridization (DDH) showed that the ISS isolates are similar to B. anthracis (88% to 90%) but distant from the B. cereus (42%) and B. thuringiensis (48%) type strains. The DDH results were supported by average nucleotide identity (>98.5%) and digital DDH (>86%) analyses. However, the collective phenotypic traits and genomic evidence were the reasons to exclude the ISS isolates from B. anthracis. Nevertheless, multilocus sequence typing and whole-genome single nucleotide polymorphism analyses placed these isolates in a clade that is distinct from previously described members of the B. cereus sensu lato group but closely related to B. anthracis. IMPORTANCE The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions.

Corrigendum: Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium

To better characterize murine intestinal microbiota, a large number (187) of Gram-positive-staining, rod- and coccoid-shaped, and facultatively or strictly anaerobic bacteria were isolated from small and large intestinal contents from mice. Based on 16S rRNA gene sequencing, a total 115 isolates formed three phylogenetically distinct clusters located within the family Erysipelotrichaceae. Group 1, as represented by strain NYU-BL-A3T, was most closely related to Allobaculum stercoricanis, with 16S rRNA gene sequence similarity values of 87.7 %. A second group, represented by NYU-BL-A4T, was most closely related to Faecalibaculum rodentium, with 86.6 % 16S rRNA gene sequence similarity. A third group had a nearly identical 16S rRNA gene sequence (99.9 %) compared with the recently described Faecalibaculum rodentium, also recovered from a laboratory mouse; however, this strain had a few differences in biochemical characteristics, which are detailed in an emended description. The predominant (>10 %) cellular fatty acids of strain NYU-BL-A3T were C16 : 0 and C18 : 0, and those of strain NYU-BL-A4T were C10 : 0, C16 : 0, C18 : 0 and C18 : 1ω9c. The two groups could also be distinguished by multiple biochemical reactions, with the group represented by NYU-BL-A4T being considerably more active. Based on phylogenetic, biochemical and chemotaxonomic criteria, two novel genera are proposed, Ileibacterium valens gen. nov., sp. nov. with NYU-BL-A3T (=ATCC TSD-63T=DSM 103668T) as the type strain and Dubosiella newyorkensis gen. nov., sp. nov. with NYU-BL-A4T (=ATCC TSD-64T=DSM 103457T) as the type strain.

Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions of the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii

A novel psychrotolerant bacterium, strain ISLP-3T, was isolated from a sample of naturally formed ice sculpture on the shore of Lake Podprudnoye in Antarctica. Cells were motile, stained Gram-positive, non-spore-forming, straight or slightly curved rods with the shape of a baseball bat. The new isolate was facultatively anaerobic and catalase-positive. Growth occurred at 3-35 °C with an optimum at 22-24 °C, 0-2 % (w/v) NaCl with an optimum at 0.3 % and pH 6.2-9.5 with an optimum at pH 7.5. Strain ISLP-3T grew on several carbon sources, with the best growth on cellobiose. The isolate possessed ureolytic activity but growth was inhibited by urea. The strain was sensitive to: ampicillin, gentamycin, kanamycin rifampicin, tetracycline and chloramphenicol. Major fatty acids were: anteiso-C15 : 0, iso-C16 : 0, C16 : 0, C14 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H4). The genomic G+C content was 69.5 mol%. The 16S rRNA gene showed 99 % sequence similarity to that of Sanguibacter suarezii ST-26T, but their recA genes shared ≤91 % sequence similarity, suggesting that this new isolate represents a novel species within the genus Sanguibacter. This conclusion was supported by average nucleotide identity, which was ≤91 % to the most closely related strain. The name Sanguibacter gelidistatuariae sp. nov. is proposed for the novel species with the type strain ISLP-3T=ATCC TSD-17T=DSM 100501T=JCM 30887T). The complete genome draft sequence of ISLP-3T was deposited under IMG OID 2657245272. Emendments to the descriptions of related taxa have been made based on experimental data from our comparative analysis.

Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone

A cultivation-based study of the microbial diversity of cellular phone screens led to the isolation of a Gram-stain-positive, aerobic, rod-shaped and non-endospore-forming bacterium, designated S2T63T, exhibiting phenotypic and genotypic characteristics unique to the type strains of closely related species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a member of Microbacterium, and most closely related to Microbacterium aurantiacum IFO 15234T and Microbacterium kitamiense Kitami C2T. The DNA-DNA relatedness values of the strain S2T63T to M. aurantiacum KACC 20510T, M. kitamiense KACC 20514Tand Microbacterium laevaniformans KACC 14463T were 65 % (±4), 29.5 % (±3) and 55.9 % (±4), respectively. The genomic DNA G+C content was 71.8 mol%. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified polar lipids. The peptidoglycan contained the amino acids glycine, lysine, alanine and glutamic acid, with substantial amounts of hydroxy glutamic acid detected, which is characteristic of peptidoglycan type B1α. The predominant menaquinones were MK-12 and MK-13. Rhamnose, fucose and galactose were the whole-cell sugars detected. The strain also showed biofilm production, estimated by using crystal violet assay. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new strain represents a novel species of the genus Microbacterium, for which the name Microbacteriumtelephonicum is proposed, with S2T63T (=MCC 2967T=KACC 18715T=LMG 29293T) as the type strain.

Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).

Williamwhitmania taraxaci gen. nov., sp. nov., a proteolytic anaerobe with a novel type of cytology from Lake Untersee in Antarctica, description of Williamwhitmaniaceae fam. nov., and emendation of the order Bacteroidales Krieg 2012

The proteolytic bacterium strain A7P-90mT was isolated from Lake Untersee, Antarctica. The anoxic water was collected from a perennially sealed (~100 millennia) glacial ice lake. Gram-stain-negative cells were 0.18-0.3×8.0-25.0 µm in size, straight, slender rods with unusual gliding motility by external, not previously reported, organelles named here as antiae. At the end of stationary phase of growth, spheroplasts were terminally formed and the cells resembled dandelions. After death, cells were helical. The isolate was an athalassic, strictly anaerobic and catalase-negative proteolytic chemoorganotroph. It was moderately psychrophilic with a temperature range for growth of 3-26 °C and an optimum at 22-23 °C. The pH range for growth was 5.5-7.8 with an optimum at 6.9. Major cellular fatty acids were branched pentadecanoic and tridecanoic acids, and saturated tetradecanoic acids. The quinone system comprised menaquinone MK-7. The strain was sensitive to all checked antibiotics and ascorbic acid. The G+C content of the genomic DNA was 42.6 mol%. Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order Bacteroidales and formed a novel family with the proposed name Williamwhitmaniaceae fam. nov. The description of the order Bacteroidales was emended accordingly. The name Williamwhitmania taraxaci gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain A7P-90mT (=DSM 100563T=JCM 30888T). The complete draft genome sequence was deposited at the Joint Genomes Institute (JGI) under number IMG OID 2654588148 and in SRA listed as SRP088197.