16S rRNA Gene Sequence Identity Research Articles

Nocardia sputorum sp. nov., an actinobacterium isolated from clinical specimens in Japan.

Two novel actinobacteria, designated IFM 12276T and IFM 12275, were isolated from clinical specimens in Japan, and their taxonomic positions were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains IFM 12276 T and IFM 12275 have completely identical 16S rRNA gene sequences and were closely related to members of the genus Nocardia. The highest 16S rRNA gene sequence similarity was observed to Nocardia beijingensis (99.6 %) and Nocarida sputi (99.6 %), followed by Nocardia niwae (99.3 %) and Nocardia araoensis (99.3 %). The whole-cell hydrolysates of strains IFM 12276T and IFM 12275 contained meso-diaminopimelic acid, arabinose and galactose. The acyl type of muramic acid was N-glycolyl. The predominant isoprenoid quinone was MK-8(H4, ω-cycl.) and the principal polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. Strains IFM 12276T and IFM 12275 contained mycolic acids that co-migrated with those from the type strain of N. niwae. These chemotaxonomic features corresponded to those of the genus Nocardia. Meanwhile, the differences in some phenotypic characteristics, along with the results of average nucleotide identity and digital DNA-DNA hybridization analyses, indicated that strains IFM 12276 T and IFM 12275 should be distinguished from the recognized species of the genus Nocardia. Therefore, these strains represent a novel species of the genus Nocardia, for which the name Nocardia sputorum sp. nov. is proposed. The type strain is IFM 12276T (=NBRC 115477T=TBRC 17096T).

Isolation of Brucella inopinata from a White's tree frog (Litoria caerulea): pose exotic frogs a potential risk to human health?

Cold-blooded hosts, particularly exotic frogs, have become a newly recognized reservoir for atypical Brucella species and strains worldwide, but their pathogenicity to humans remains largely unknown. Here we report the isolation and molecular characterization of a B. inopinata strain (FO700662) cultured from clinical samples taken from a captive diseased White's Tree Frog (Litoria caerulea) in Switzerland. The isolation of B. inopinata from a frog along with other reports of human infection by atypical Brucella raises the question of whether atypical Brucella could pose a risk to human health and deserves further attention. The investigations included histopathological analysis of the frog, bacterial culture and in-depth molecular characterization of strain FO700662 based on genome sequencing data. Originally identified as Ochrobactrum based on its rapid growth and biochemical profile, strain FO700622 was positive for the Brucella- specific markers bcsp31 and IS711. It showed the specific banding pattern of B. inopinata in conventional Bruce-ladder multiplex PCR and also had identical 16S rRNA and recA gene sequences as B. inopinata. Subsequent genome sequencing followed by core genome-based MLST (cgMLST) analysis using 2704 targets (74% of the total chromosome) revealed only 173 allelic differences compared to the type strain of B. inopinata BO1T, while previously considered the closest related strain BO2 differed in 2046 alleles. The overall average nucleotide identity (ANI) between the type strain BO1T and FO700622 was 99,89%, confirming that both strains were almost identical. In silico MLST-21 and MLVA-16 also identified strain FO700662 as B. inopinata. The nucleotide and amino acid-based phylogenetic reconstruction and comparative genome analysis again placed the isolate together with B. inopinata with 100% support. In conclusion, our data unequivocally classified strain FO700622, isolated from an exotic frog, as belonging to B. inopinata.

Description of Dellaglioa carnosa sp. nov., a novel species isolated from high-oxygen modified-atmosphere packaged meat

The study provides a taxonomic characterization of three bacterial strains isolated from high-oxygen modified-atmosphere packaged beef from Germany. The strains of the novel species shared identical 16S rRNA gene sequence to the closely related type strain of Dellaglioa algida. However, the in-silico DNA-DNA hybridization (DDH) values indicate that they belong to a different genomic species. The in silico DDH estimate value between TMW 2.2523T and the type strain of Dellaglioa algida DSM 15638T was only 63.2 %. The whole genome average nucleotide identity blast (ANIb) value of 95.1 % between TMW 2.2523T and the closely related type strain of D. algida was within the recommended threshold value of 95–96 % for bacterial species delineation. Additionally, the phylogenomic analyses based on multi locus sequence alignment (MLSA) showed that strain TMW 2.2523T and additional strains TMW 2.2444 and TMW 2.2533 formed a monophyletic group separate from D. algida strains. Furthermore, tyrosine decarboxylase activity could be attributed to strains of the new proposed species. The results of this polyphasic approach support the affiliation of these strains to a novel species within the genus Dellaglioa for which we propose the name Dellaglioa carnosa sp. nov. The designated respective type strain is TMW 2.2523T (DSM 114968T = LMG 32819T).

Description of Alkalimarinus coralli sp. nov., isolated from tissue of the coral Pocillopora damicornis.

Three novel strains, SCSIO 12582T, SCSIO 12638 and SCSIO 12817, were isolated from tissue of the coral Pocillopora damicornis collected from Hainan province, PR China. The results of phylogenetic analysis based on 16S rRNA genes revealed that these three isolates showed nearly identical 16S rRNA gene sequences (99.86 %-99.93 %), forming a separate monophyletic cluster within the genus Alkalimarinus and closely related to Alkalimarinus sediminis FA028T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values among the three strains were 99.94 %-99.96 % and 100 %, respectively, indicating that these three isolates were affiliated with the same species. Analysis of the 16S rRNA gene sequence revealed that SCSIO 12582T (representative of the novel isolates) exhibited 98.49 % sequence similarity to A. sediminis FA028T. The ANI and dDDH values between SCSIO 12582T and A. sediminis FA028T were 74.81 % and 18.90 % respectively. These three isolates were facultatively anaerobic, Gram-stain-negative, rod shaped and catalase- and oxidase-positive. The DNA G+C content of SCSIO 12582T was 45.82 %. The major respiratory quinone was Q-9. The main cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 1ω9c. The polar lipids present were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of the results of the phylogenetic, chemotaxonomic, phenotypic and genomic analysis, it was evident that isolates SCSIO 12582T, SCSIO 12638 and SCSIO 12817 represent a novel species of the genus Alkalimarinus, for which the name Alkalimarinus coralli sp. nov. is proposed. The type strain is SCSIO 12582T (=JCM35228T=GDMCC1.3061T).

A Limited Effect of Chronic Renal Insufficiency on the Colon Microbiome.

A Limited Effect of Chronic Renal Insufficiency on the Colon Microbiome.

At the threshold of symbiosis: the genome of obligately endosymbiotic 'Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain.

Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.

Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum.

Two endophytic bacteria, designated strains CQZ9-1T and MQZ9-1, were isolated from semi-mangrove plant Acrostichum aureum collected from Maowei Sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, PR China. The two strains possessed almost identical 16S rRNA gene sequences (99.7 %). The average nucleotide identity (ANI), average amino acid identity (AAI) and the digital DNA-DNA hybridization (dDDH) values between the two strains were 100 %, indicating that they represented the same species. The 16S rRNA gene sequence similarities between strains CQZ9-1T, MQZ9-1 and the most closely related type strains, Jiella mangrovi KSK16Y-1T, Jiella sonneratiae MQZ13P-4T and Jiella endophytica CBS 5Q-3T were 98.0-98.1, 97.3-97.4 and 97.3-97.4 %, respectively. The results of phylogenetic analyses based on 16S rRNA gene sequences and genome sequences indicated that CQZ9-1T and MQZ9-1 formed a distinct lineage with J. endophytica CBS5Q-3T, Jiella pacifica 40Bstr34T, J. mangrovi KSK16Y-1T, J. sonneratiae MQZ13P-4T, Jiella aquimaris JCM 30119T and J. aquimaris 22II-16-19i. The draft genomes of strains CQZ9-1T and MQZ9-1 were 4 162 933 bp and 4 164 266 bp in size, respectively, and their DNA G+C contents were both 63.8 %. Comparative genome analysis of the two strains and the type strains of related species revealed ANI, AAI and dDDH values below the cut-off levels of 95-96, 95.5 and 70 %, respectively. The ubiquinone detected in CQZ9-1T was Q-10. The major cellular fatty acid of strains CQZ9-1T and MQZ9-1 was found to be C18:1ω7c. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that CQZ9-1T and MQZ9-1 represent a novel species of the genus Jiella, for which the name Jiella flava sp. nov. is proposed. The type strain is CQZ9-1T (= CGMCC 1.18725T = JCM 34331T).

Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica.

Strains P8930T and 478 were isolated from Antarctic glaciers located on James Ross Island and King George Island, respectively. They comprised Gram-stain-negative short rod-shaped cells forming pink pigmented colonies and exhibited identical 16S rRNA gene sequences and highly similar MALDI TOF mass spectra, and hence were assigned as representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences assigned both isolates to the genus Pedobacter and showed Pedobacter frigidisoli and Pedobacter terrae to be their closest phylogenetic neighbours, with 97.4 and 97.2 % 16S rRNA gene sequence similarities, respectively. These low similarity values were below the threshold similarity value of 98.7%, confirming the delineation of a new bacterial species. Further genomic characterization included whole-genome sequencing accompanied by average nucleotide identity (ANI) and digital DNA-DNA hybridization calculations, and characterization of the genome features. The ANI values between P8930T and P. frigidisoli RP-3-11T and P. terrae DSM 17933T were 79.7 and 77.6 %, respectively, and the value between P. frigidisoli RP-3-11T and P. terrae DSM 17933T was 77.7 %, clearly demonstrating the phylogenetic distance and the novelty of strain P8930T. Further characterization included analysis of cellular fatty acids, quinones and polar lipids, and comprehensive biotyping. All the obtained results proved the separation of strains P8930T and 478 from the other validly named Pedobacter species, and confirmed that they represent a new species for which the name Pedobacter fastidiosus sp. nov. is proposed. The type strain is P8930T (=CCM 8938T=LMG 32098T).

Pinisolibacter aquiterrae sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus Pinisolibacter.

Two Gram-reaction-negative strains, designated as B13T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to Pinisolibacter ravus E9T (97.36 %) and Siculibacillus lacustris SA-279T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13T and MA2-2 were C18 : 1 ω7c/C18 : 1 ω6c, C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The major ubiquinone of strain B13T was Q10, while the major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13T and MA2-2 are members of the genus Pinisolibacter and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13T (=LMG 32346T=NCAIM B.02665T).

Paenibacillus sinensis sp. nov., a nitrogen-fixing species isolated from plant rhizospheres.

Two strains HN-1T and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1T and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472T and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1T with P. stellifer DSM 14472T was 90.69, which was below the recommended threshold value (< 95-96% ANI). The dDDH showed 42.1% relatedness between strain HN-1T and P. stellifer DSM 14472T, which was lower than the recommended threshold value (dDDH < 70%). The strain HN-1T contain anteiso-C15:0 as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472T, strain HN-1T or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1T or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1T (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.

Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity

Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794T, Streptomyces laculatispora NRRL B-24909T, and Streptomyces brevispora NRRL B-24910T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04T (=DSM 111306T = CCM 9048T) as the type strain.

Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges

Two novel Rhodococcus strains, LHW50502T and LHW51113T, were isolated from marine sponges obtained on Xisha Island, Hainan Province, PR China. Rods and cocci, typical characteristics of the genus Rhodococcus, were observed. The strains contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall hydrolysates and galactose, arabinose, ribose and glucose as the whole-cell sugars. The major fatty acid identified was C16 : 0. MK-8(H4) was the predominat menaquinone of both strains. Stains LHW50502T and LHW51113T had almost identical (99.6 %) 16S rRNA gene sequences but shared relatively low similarities with previously characterized Rhodococcus species (well below 98.7 %). The results of phylogenetic analysis supported their closest relationship; however, the average nucleotide identity and digital DNA-DNA hybridization values between these two strains indicated that they belonged to distinct species. Taken together, the results of this study indicate that strains LHW50502T and LHW51113T represent two novel species of the genus Rhodococcus, for which the names Rhodococcus spongiicola sp. nov. (type strain LHW50502T=DSM 106291T=CCTCC AA 2018033T) and Rhodococcus xishaensis sp. nov. (type strain LHW51113T=DSM 106204T=CCTCC AA 2018034T) are proposed.

Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize.

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

Emerging Patterns of Microbial Functional Traits.

Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.

Salegentibacter maritimus sp. nov., isolated from marine coastal sediment

Two bacterial strains were isolated from a marine sediment sample taken from Jingzi Wharf, Weihai, China. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. The two strains possessed almost identical 16S rRNA gene sequences (99.9 %). However, RAPD-PCR fingerprint patterns discriminated that they were not from one clonal origin. The average nucleotide identity (ANI) value and the digital DNA-DNA hybridization (dDDH) value between the two strains were 98.3 % and 85.4 %, respectively, suggestingthat they belonged to the same species. On the basis of the result of phylogenetic analysis of the 16S rRNA gene sequences, the two strains belonged to the genus Salegentibacter and were closely related to S. holothuriorum KCTC 12371T (98.6 %) and S. salegens DSM 5424T (98.2–98.3 %). The ANI and dDDH clearly separated strains F63223T and F60176 from the the most related type strains with values below the thresholds for species. The genome sizes of strains F63223T and F60176 were approximate 3.89 and 3.59 Mbp, respectively. The strain F63223T had 3,335 predicted genes with DNA G + C content of 35.6 %. The major respiratory quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and one unidentified lipid. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic classification and genome analysis, the two isolates could be considered to represent a novel species of the genus Salegentibacter, for which the name Salegentibacter maritimus sp. nov., is proposed, with F63223T (=MCCC 1H00433T = KCTC 82417T) as the type strain.

Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra

Two actinobacteria, strains NF3 and NH11T, isolated from a pine forest soil, near Torun, Poland were examined for diverse chemotaxonomic and morphological properties that placed them in the genus Catenulispora. They produced an extensively branched stable mycelium, contained LL-diaminopimelic acid as the diamino acid of the peptidoglycan, arabinose as the diagnostic whole-organism sugar, tetra-, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units as the predominant isoprenologues, iso-C16:0 and anteiso-C17:0 as major fatty acids, and formed a well supported clade within the Catenulispora 16S rRNA gene tree together with Catenulispora acidiphila DSM 44928T and Catenulispora rubra DSM 44948T sharing sequence similarities with the latter of 98.8 and 99.0%, respectively. The sizes of whole genome sequences generated for the isolates and the C. rubra strain ranged from 11.20 to 12.80 Mbp with corresponding in silico DNA G+C values of 69.9–70.0%. The isolates and the C. acidiphila and C. rubra strains formed a well supported branch in the actinobacterial phylogenomic tree. Isolates NF3 and NH11T belong to the same species as they have identical 16S rRNA gene sequences, share many chemotaxonomic, cultural and phenotypic features and show very high average nucleotide identity (ANI) and digital DNA:DNA relatedness (dDDH) similarities. They can be distinguished from their closest phylogenomic neighbours by using a combination of chemotaxonomic and phenotypic properties and by ANI and dDDH values well below the thresholds of these metrics used to assign closely related strains to different species. Consequently, we propose that the isolates be classified as a new Catenulispora species, Catenulispora pinisilvae sp. nov., the type strain is NH11T (=DSM 111109T =PCM 3046T). An emended description is given for C. rubra based on data acquired in the present study. Analyses of the draft genomes of the isolates and the C. acidiphila and C. rubra strains revealed the presence of many biosynthetic gene clusters with the potential to synthesize novel drug-like metabolites. In vitro screens showed that the isolates inhibited the growth of Gram-positive bacteria and wheat pathogens belonging to the genus Fusarium.

Chromobacterium paludis sp. nov., a novel bacterium isolated from a Chesapeake Bay marsh.

Two isolates of Gram-reaction-negative, motile, violet-pigmented bacteria were isolated from a small pool in marshland near the mouth of the Nanticoke River in Maryland, USA. The isolates IIBBL 257-1T and IIBBL 257-2 had identical 16S rRNA gene sequences as determined by PCR, and highly similar fatty acid and biochemical profiles. The 16S rRNA gene sequences indicated the isolates belonged to the genus Chromobacterium. Genomic sequencing of IIBBL 257-1T revealed a genome of 4.27 Mb, with a G+C content of 63.6 %. Whole genome comparisons with other members of the Chromobacterium using JSpecies and the genome blast distance phylogeny approach indicated that among described species, IIBBL 257-1T was most closely related to C. amazonense and C. phragmitis. Comparison of the IIBBL 257-1T genome with those of type strains of these species resulted in ANIb and dDDH values of ca. 85 and 30 %, respectively, for both. These results demonstrate that IIBBL 257-1T and IIBBL 257-2 represent a new taxon within the genus Chromobacterium. We propose the name Chromobacterium paludis sp. nov. for this taxon; the type strain is IIBBL 257-1T (=NRRL B-65555T=JCM 33770T).

Staphylococcus borealis sp. nov., isolated from human skin and blood

When analysing a large cohort of Staphylococcus haemolyticus, using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as S. haemolyticus based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to S. haemolyticus, these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA-DNA hybridization <70 %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus Staphylococcus and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48T, is deposited in the Culture Collection University of Gothenburg (CCUG 73747T) and in the Spanish Type Culture Collection (CECT 30011T).

Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes.

Two morphologically similar halophilic strains, named USBA 874 and USBA 960T, were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. Both isolates had non-spore-forming, Gram-stain-negative and motile cells that grew aerobically. The strains grew optimally at 30 °C, pH 7.0 and with 25 % NaCl (w/v). The isolates showed almost identical 16S rRNA gene sequences (99.0 % similarity). The predominant quinones of USBA-960T were Q-8, Q-7 and Q-9. The major cellular fatty acids were C19 : 0 cyclo ω8c, C18 : 0 and C16 : 0. According to 16S rRNA gene sequencing, the closest phylogenetic relatives are Salinisphaera species (similarity between 93.6 and 92.3 %), Abyssibacter profundi OUC007T (88.6 %) and Oceanococcus atlanticus 22II-S10r2T (88.7 %). In addition, the result of genome blast distance phylogeny analysis between strains USBA 874 and USBA 960T, Salinisphaera halophila (YIM 95161T), Salinisphaera shabanensis (E1L3AT), Salinisphaera orenii (MK-B5T) and Salinisphaera japonica (YTM-1T) was 18.5 %. Other in silico species delineation analyses also showed low identity such as ANIb and ANIm values (<69.0 and <84.0 % respectively), TETRA (<0.81) and AAI values (<0.67). Genome sequencing of USBA 960T revealed a genome size of 2.47 Mbp and a G+C content of 59.71 mol%. Phylogenetic analysis of strains USBA 874 and USBA 960T indicated that they formed a different lineage within the family Salinisphaeraceae. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with identity at whole genome level, it can be concluded that strains USBA 960T and USBA 874 represent a novel genus of the family Salinisphaeraceae and the name Salifodinibacter halophilus gen. nov., sp. nov. is proposed. The type strain is USBA 960T (CMPUJ U095T=CECT 30006T).

Lactococcus carnosus sp. nov. and Lactococcus paracarnosus sp. nov., two novel species isolated from modified-atmosphere packaged beef steaks.

As part of a study investigating the spoilage microbiome of modified-atmosphere packaged beef from Germany, four novel strains of lactic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they could not be assigned to known species. The isolates were Gram-staining-positive, coccoid, facultatively anaerobic, non-motile, catalase-negative and oxidase-negative. Morphological, physiological and phylogenetic analysis revealed a distinct lineage within the genus Lactococcus, with Lactococcus piscium and Lactococcus plantarum as closest relatives. Results indicated that they represented two different novel species with two strains, (TMW 2.1612T/TMW 2.1613 and TMW 2.1615T/TMW 2.1614), respectively. The two strains of both novel species shared identical 16S rRNA gene sequences but a MLSA allowed their intraspecies differentiation. The 16S rRNA gene sequences of TMW 2.1612T and TMW 2.1615T had a similarity of 99.85 % to each other and a similarity of 99.85 and 99.78 % the most closely related type strain of Lactococcus piscium, respectively. However, the ANIb value between the respective type strains TMW 2.1612T and TMW 2.1615T, and the type strain of Lactococcus piscium was only 94.3 and 92.0 %, respectively, and 92.9 % between TMW 2.1612T and TMW 2.1615T. The in silico DDH estimate value between the respective type strain TMW 2.1612T and TMW 2.1615T and the most closely related type strain of Lactococcus piscium was only 59.9 and 48.9 %, respectively, and 51.1 % between TMW 2.1612T and TMW 2.1615T. Peptidoglycan type of strain TMW 2.1612T is Lys-Thr-Ala and major fatty acids are summed feature 8 and C16 : 0. Peptidoglycan type of strain TMW 2.1615T is Lys-Ala and major fatty acids are C16 : 0, C19 : 0cyclo ω8c and summed feature 8. On the basis of polyphasic evidence, the meat isolates represent two novel species of the genus Lactococcus, for which the names Lactococcus carnosus sp. nov and Lactococcus paracarnosus sp. nov are proposed. The designated respective type strains are TMW 2.1612T (=DSM 111016T =CECT 30115T) and TWM 2.1615T (=DSM 111017T =CECT 30116T).