Lysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity

An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to Lysinibacillus fusiformis NRRL NRS-350T (99.7%) and Lysinibacillus sphaericus NRRL B-23268T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15: 0 (52.3%), anteiso-C15: 0 (14.8%), C16:1ω7C alcohol (11.2%), and C16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of Lysinibacillus revealed this strain formed a distinct monophyletic clade with the nearest neighbor being Lysinibacillus fusiformis. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus pinottii sp. nov. is proposed, with type strain PB211T (= NRRL B-65672T, = CCUG 77181T).

Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov

A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump

A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus absianus and Lacticaseibacillus daqingensis. The main fatty acids of the strain is the C_18 : 1ω9c and C_16 : 0. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lac21^T (=KCTC 21185=JCM 34953) represents a novel species. The name Lacticaseibacillus kribbianus sp. nov. is proposed.

Green Chemistry Based Gold Nanoparticles Synthesis Using the Marine Bacterium Lysinibacillus odysseyi PBCW2 and Their Multitudinous Activities

Green chemistry has paved an 'avant-garde avenue' in the production and fabrication of eco-friendly stable nanoparticles employing the utilization of biological agents. In the present study we present the first report on the potential of the marine bacterium Lysinibacillus odysseyi PBCW2 for the extracellular production of gold nanoparticles (AuNPs). Utilizing a variety of methods, AuNPs in the cell-free supernatant of L. odysseyi (CFS-LBOE) were identified and their antioxidant, antibacterial, and dye-degrading properties were examined. The visual coloring of the reaction mixture to a ruby red hue showed the production of LBOE-AuNPs; validated by means of XRD, TEM, SEM, XRD, DLS, TGA, and FT-IR analysis. Additionally, the 2,2-diphenyl-1-picrylhydrazyl technique and the well diffusion assay were used to examine their dose-dependent antioxidant and antibacterial activity. These biogenic LBOE-AuNPs showed 91% dye degradation efficiency during catalytic reduction activity on BTB dye, demonstrating their versatility as options for heterogeneous catalysis.

Characterization of Bacterial Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic, Metatranscriptomic, and Culturing Techniques

The postmortem microbiome has recently moved to the forefront of forensic research, and many studies have focused on the idea that predictable fluctuations in decomposer communities could be used as a “microbial clock” to determine time of death. Commonly, the oral microbiome has been evaluated using 16S rRNA gene sequencing to assess the changes in community composition throughout decomposition. We sampled the hard palates of three human donors over time to identify the prominent members of the microbiome. This study combined 16S rRNA sequencing with whole metagenomic (MetaG) and metatranscriptomic (MetaT) sequencing and culturing methodologies in an attempt to broaden current knowledge about how these postmortem microbiota change and might function throughout decomposition. In all four methods, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the dominant phyla, but their distributions were insufficient in separating samples based on decomposition stage or time or by donor. Better resolution was observed at the level of genus, with fresher samples from decomposition clustering away from others via principal components analysis (PCA) of the sequencing data. Key genera in driving these trends included Rothia; Lysinibacillus, Lactobacillus, Staphylococcus, and other Firmicutes; and yeasts including Candida and Yarrowia. The majority of cultures (89%) matched to sequences obtained from at least one of the sequencing methods, while 11 cultures were found in the same samples using all three methods. These included Acinetobacter gerneri, Comamonas terrigena, Morganella morganii, Proteus vulgaris, Pseudomonas koreensis, Pseudomonas moraviensis, Raoutella terrigena, Stenotrophomonas maltophilia, Bacillus cereus, Kurthia zopfii, and Lactobacillus paracasei. MetaG and MetaT data also revealed many novel insects as likely visitors to the donors in this study, opening the door to investigating them as potential vectors of microorganisms during decomposition. The presence of cultures at specific time points in decomposition, including samples for which we have MetaT data, will yield future studies tying specific taxa to metabolic pathways involved in decomposition. Overall, we have shown that our 16S rRNA sequencing results from the human hard palate are consistent with other studies and have expanded on the range of taxa shown to be associated with human decomposition, including eukaryotes, based on additional sequencing technologies.

Lacticaseibacillus absianus sp. nov., isolated from the cecum of a mini-pig

A rod-shaped, facultative anaerobic, Gram-stain-positive bacteria, isolated from the cecum of a mini-pig, was designated as strain YH-lac23^T. Analysis of 16S rRNA gene sequences revealed that the strain was closely related to Lacticaseibacillus daqingensis JCM 33273^T (97.9 %), Lacticaseibacillus porcinae KCTC 21027^T (96.2 %) and Lacticaseibacillus manihotivorans KCTC 21010^T (95.7 %). Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. daqingensis. The average nucleotide identity value for YH-lac23^T and its most closely related strain (L. daqingensis) is 80.7 %. The main fatty acids are C_18 : 1ω9c and C_16 : 0. The cell wall contains the peptidoglycan of meso-diaminopimelic acid. The G+C content of the genomic DNA is 59.8 mol%. In view of the chemotaxonomic, phenotypic and phylogenetic properties, YH-lac23^T (=KCTC 25006=JCM 33998) represents a novel taxon. The name Lacticaseibacillus absianus sp. nov. is proposed.

Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig

A Gram-stain-positive, facultative anaerobic, rod-shaped bacteria isolated from the small intestine of a mini pig was designated as strain YH-lac9^T. 16S rRNA gene sequence analysis revealed that the strain belongs to the genus Lentilactobacillus and is closely related to Lentilactobacillus senioris JCM 17472^T, Lentilactobacillus rapi JCM 15042^T and Lentilactobacillus diolivorans JCM 13927^T, with 97.6, 96.2 and 95.7 % sequence similarity, respectively. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. senioris, supporting the results of 16S rRNA gene sequences analysis. The average nucleotide identity value for YH-lac9^T and the most closely related strain is 74.1 %. The main fatty acids are C_18 : 1ω9c, summed feature 7, C_16 : 0 and summed feature 8. The G+C content of the genomic DNA is 37.8 mol%. In view of its chemotaxonomic, phenotypic and phylogenetic properties, YH-lac9^T (=KCTC 25005=JCM 33997) represents a novel taxon. The name Lentilactobacillus kribbianus sp. nov. is proposed.

Lysinibacillus antri sp. nov., isolated from cave soil

A Gram-stain-positive, motile, rod-shaped and endospore-forming strain, SYSU K30002^T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-west China. SYSU K30002^T grew at 28-40 °C (optimum, 37 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-4 % (w/v) NaCl (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4α (Lys-Asp). The cell-wall sugars of SYSU K30002^T were ribose, galactose and mannose, and MK-7 was the menaquinone. The major fatty acids were iso-C_15 : 0, C_16 : 1 ω7c alcohol and iso-C_16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. The G+C content of the genomic DNA was 36.1 mol%. The average nucleotide identity values between SYSU K30002^T and its closest relatives were below the cut-off level (95-96 %) for species delineation. Based on phenotypic, chemotaxonomic and genome comparisons, strain SYSU K30002^T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillusantri sp. nov. is proposed. The type strain is SYSU K30002^T (=KCTC 33955^T=CGMCC 1.13504^T).

Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

Paenibacillus oralis sp. nov., Isolated from Human Subgingival Dental Plaque of Gingivitis Lesion

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20^T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593^T (97.7% similarity) and Paenibacillus macerans ATCC 8244^T (97.6% similarity). Draft genome of strain ChDC PVNT-B20^T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3 mol%. Average nucleotide identity values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20^T were anteiso-C_15:0 (43.4%), C_16:0 (16.6%), iso-C_16:0 (14.4%), and anteiso-C_17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20^T (= KCOM 3021^T = JCM 33462 ^T).

Complete Genome Sequence of Lysinibacillus sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore

Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

Lysinibacillus sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.

Isolation and characterization of a novel piezotolerant bacterium Lysinibacillus yapensis sp. nov., from deep-sea sediment of the Yap Trench, Pacific Ocean

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03^T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15-50°C (optimum 37°C), pH 5-10.5 (optimum 7), 0-5% NaCl (optimum 1%, w/v) and 0.1-50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03^T was a member of the genus Lysinibacillus. Strain YLB-03^T was closely related to Lysinibacillus sinduriensis BLB-1^T and Lysinibacillus chungkukjangi 2RL3-2^T (98.4%), Lysinibacillus halotolerans LAM-612^T (98.0%), Lysinibacillus telephonicus KT735049^T (97.5%), Lysinibacillus endophyticus C9^T (97.5%), Lysinibacillus composti NCCP-36^T and Lysinibacillus massiliensis 4400831^T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03^T and closely related type strains were 73.7-76.3% and 34.7-38.7%, respectively. The principal fatty acids were anteiso-C_15:0 and iso-C_15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03^T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03^T (= MCCC 1A12698^T = JCM 32871^T).

Lysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant

A strain of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from rhizospheric soil of a pepper plant when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain, PB300^T, is closely related to Lysinibacillus macroides DMS 54^T (99.6%) and Lysinibacillus xylanilyticus DSM 23493^T (99.4%). In phenotypic characterisation, the novel strain was found to grow between 15 and 40 °C and tolerate up to 10% (w/v) NaCl. Furthermore, the strain was found to grow in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C_15 : 0 (56.6 %), anteiso-C_15 : 0 (14.6%), C_16 :1ω7C alcohol (9.3%) and C_16 : 0 (7.1%). The cell wall peptidoglycan contains lysine-aspartic acid, as in its close relatives. A draft genome was completed and the DNA G + C content was determined to be 37.5% (mol content). A phylogenomic analysis of the core genome of the new strain and 5 closely related type strains of the genus Lysinibacillus revealed that this strain formed a distinct monophyletic clade with the nearest neighbour being Lysinibacillus boronitolerans. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed relationships for the new strain were below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus capsici sp. nov. is proposed, with type strain PB300^T (= NRRL B-65515^T, = CCUG 72241^T).

Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces

Two isolates of a Gram-positive, non-motile, coccoid or oval-shaped anaerobic bacterium, designated strains N6H1-15^T and YH1_16, were isolated from faecal samples obtained from a mature dog. Analysis of 16S rRNA gene sequences indicated that the isolates belonged to the Blautia coccoidesrRNA gene group (cluster XIVa) and were closely related to Blautia hansenii KCTC 5951^T, Blautia stercoris KCTC 5981^T, Blautia producta producta KCTC 3695^T and B. coccoides DSM 15327^T, with 96.7, 94.4, 94.2 and 93.9 % sequence similarity, respectively. The two isolates contained m-diaminopimelic acid within their peptidoglycans. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the major fatty acids were C16 : 0 (18.5 %), C16 : 0 (18.0 %) and C18 : 1cis 9 (16.2 %). The predominant metabolic end products of glucose fermentation were acetic and lactic acids, and the G+C content was 44.2 mol%. Thus, the polyphasic data suggest that the two new isolates represent a new species, proposed as Blautia argi sp. nov. The type strain is N6H1-15^T (=KCTC 15426=JCM 31394).

Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides

Three bacterial isolates from human faeces, YS-aM39^T, R2F3-3-3^T and R2F3-5-1, were characterized as Gram-negative, strictly anaerobic, non-spore-forming, non-motile, and rod-shaped. Isolate YS-aM39^T formed a distinct line of descent, showing greatest 16S rRNA gene sequence relatedness with R2F3-3-3^T (97.5 %), R2F3-5-1 (97.5 %), Bacteroides ovatus (98.8 %) and Bacteroides xylanisolvens (97.2 %). Isolates R2F3-3-3^T and R2F3-5-1 also formed a distinct line of descent, sharing greatest 16S rRNA gene sequence relatedness with B. ovatus (98.2 %) and B. xylanisolvens (97.2 %). The DNA G+C content of YS-aM39^T was 44.8 mol%, that of R2F3-3-3^T was 42.4 mol% and that of R2F3-5-1 was 42.6 mol%. The respiratory quinone of all three isolates was menaquinone MK-10. Polar lipid analysis identified phosphatidylethanolamine as the major lipid. The predominant fatty acids in all three isolates were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 3-OH and iso-C17 : 0 3-OH. The major end products of glucose fermentation were acetic acid, lactic acid and formic acid. DNA-DNA hybridization data indicated that two isolates, YS-aM39^T and R2F3-3-3^T, represent a species distinct from B. ovatus and B. xylanisolvens. Finally, in this study, the two isolates represented two new species in the genus Bacteroides, for which we propose the names Bacteroides koreensis sp. nov. (type strain, YS-aM39^T=KCTC 15520^T=JCM 31393^T) and Bacteroides kribbi sp. nov. (type strain, R2F3-3-3^T=KCTC 15460^T=JCM 31391^T).

Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone

A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10-55 °C) and at pH 7.0 (5.0-9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA-DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).

'Lysinibacillus saudimassiliensis' sp. nov., a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia

We report here the main characteristics of 'Lysinibacillus saudimassiliensis' strain 13S34_air^τ (CSUR = P1222), a new species of the Lysinibacillus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5)

A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7

Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the newly sequenced genome and the ones previously reported for Colombian isolates L. sphaericus OT4b.31, CBAM5 and OT4b.25, with the inclusion of L. sphaericus C3-41 that has been used as a reference genome for most of previous genome sequencing projects. We concluded that L. sphaericus III(3)7 is highly similar with strain OT4b.25 and shares high levels of synteny with isolates CBAM5 and C3-41.

Lysinibacillus xyleni sp. nov., isolated from a bottle of xylene

A Gram-staining-positive, solvent-tolerating (acetophenone, benzene, toluene, xylene and hexane), aerobic, non-motile, terminal endospore-forming, rod-shaped bacterium was isolated from a bottle of xylene. The strain, designated JC22(T), was found to be oxidase and catalase positive. The strain was able to tolerate solvents with different log p values like acetophenone (log P = 1.5), benzene (log P = 2.0), toluene (log P = 2.5), xylene (log P = 3.2) and hexane (log P = 3.4), though it could not use them as sole carbon sources. Based on the 16S rRNA gene sequence analysis, strain JC22(T) was identified as belonging to the genus Lysinibacillus and was most closely related to Lysinibacillus sinduriensis BLB-1(T) (98.1 %), Lysinibacillus halotolerans LAM612(T) (97.8 %), Lysinibacillus chungkukjangi 2RL3-2(T) (97.6 %) and Lysinibacillus xylanilyticus XDB9(T) (97.1 %). The DNA-DNA relatedness of strain JC22(T) with the type strains of closest species was <30 %. Strain JC22(T) grew chemoorganoheterotrophically with an optimal pH of 7-8 (range 6-10) at 35-37 °C (range 25-40 °C). The DNA G+C content was 41.2 mol%. The major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C16:0. Cell wall peptidoglycan type was determined to be A4α (L-Lys-D-Asp). Predominant quinone system was MK-7 with moderate amounts of MK-6, MK-6(H2) and MK-7(H2). Polar lipids of strain JC22(T) contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. On the basis of morphological, physiological, genetic, phylogenetic and chemotaxonomical analyses, we conclude that strain JC22(T) be assigned the status of novel species of the genus Lysinibacillus for which the name Lysinibacillus xyleni sp. nov. is proposed. Type strain of the species is JC22(T) (= CCUG 57912(T) = KCTC 13604(T) = NBRC 105753(T) = DSM 23555(T)).

Lysinibacillus cresolivorans sp. nov., an m-cresol-degrading bacterium isolated from coking wastewater treatment aerobic sludge

A Gram-stain-positive, rod-shaped, facultatively anaerobic, endospore-forming bacterium (designated strain SC03T) was isolated from the aerobic treatment sludge of a coking plant (Shaoguan City, China). The optimal pH and temperature for growth were pH 7.0 and 35 °C. On the basis of 16S rRNA gene sequence analysis, strain SC03T was related to the genus Lysinibacillus and the similarity between strain SC03T and the most closely related type strain, Lysinibacillus macroides LMG 18474T, was 94.4 %. The genomic G+C content of the DNA of strain SC03T was 41.2 mol%. Chemotaxonomic data supported the affiliation of strain SC03T to the genus Lysinibacillus. These properties include MK-7 as the predominant menaquinone; iso-C15 : 0 and iso-C16 : 0 as major fatty acids; A4α (l-Lys-d-Asp) as the cell-wall peptidoglycan type; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine plus three unknown phospholipids as polar lipids. The phenotypic, phylogenetic and chemotaxonomic characters enable the differentiation of strain SC03T from recognized Lysinibacillus species. Thus, strain SC03T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus cresolivorans sp. nov. is proposed. The type strain is SC03T ( = NRRL B-59352T = CCTCC M 208210T).

Lysinibacillus louembei sp. nov., a spore-forming bacterium isolated from Ntoba Mbodi, alkaline fermented leaves of cassava from the Republic of the Congo

Investigation of the microbial diversity of Ntoba Mbodi, an African food made from the alkaline fermentation of cassava leaves, revealed the presence of a Gram-positive, catalase-positive, aerobic, motile and rod-shaped endospore-forming bacterium (NM73) with unusual phenotypic and genotypic characteristics. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Lysinibacillus meyeri WS 4626T (98.93%), Lysinibacillus xylanilyticus XDB9T (96.95%) and Lysinibacillus odysseyi 34hs-1T (96.94%). The DNA-DNA relatedness of the isolate with L. meyeri LMG 26643T, L. xylanilyticus DSM 23493T and L. odysseyi DSM 18869T was 41%, 16% and 15%, respectively. The internal transcribed spacer-PCR profile of the isolate was different from those of closely related bacteria. The cell-wall peptidoglycan type was A4α, L-Lys-D-Asp and the major fatty acids were iso-C15:0, anteiso-C15:0, anteiso-C17:0 and iso-C17:0 and iso-C17:1ω10c. The polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphoaminolipid, aminolipid, two phospholipids and two unknown lipids. The predominant menaquinones were MK-7 and MK-6. Ribose was the only whole-cell sugar detected. The DNA G+C content was 38 mol%. Based on the results of the phenotypic and genotypic characterization, it was concluded that the isolate represents a novel species of the genus Lysinibacillus, for which the name of Lysinibacillus louembei sp. nov. is proposed. NM73T ( = DSM 25583T = LMG 26837T) represents the type strain.

Lysinibacillus acetophenoni sp. nov., a solvent-tolerant bacterium isolated from acetophenone

A Gram-stain-positive, solvent-tolerating, aerobic, rod-shaped bacterium that formed terminal endospores was isolated from the organic solvent acetophenone. The strain, designated JC23T, was oxidase- and catalase-positive. The strain grew in the presence of a wide range of organic solvents with partition coefficients (log p values) between 1 and 4, which are exceptionally toxic to micro-organisms. Based on 16S rRNA gene sequence analysis, strain JC23T was identified as belonging to the genus Lysinibacillus and was most closely related to Lysinibacillus manganicus Mn1-7T (98.5 % similarity), L. massiliensis 440831T (97.2 %) and L. chungkukjangi 2RL3-2T (96.8 %). DNA–DNA relatedness of strain JC23T with the type strains of the closest species was <39 %. Strain JC23T grew chemo-organoheterotrophically with optimal growth at pH 7 (range pH 6–9) and at 35 °C (range 25–40 °C). The DNA G+C content was 41 mol%. Major cellular fatty acids of strain JC23T were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The cell-wall peptidoglycan type was determined to be A4α (l-Lys–d-Asp), which is in agreement with the cell-wall characteristics of the genus Lysinibacillus . The predominant quinone system was MK-7. Polar lipids of strain JC23T included diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, β-gentiobiosyldiacylglycerol, two unidentified phospholipids and two unidentified lipids. On the basis of our morphological, physiological, genetic, phylogenetic and chemotaxonomic analyses, we conclude that strain JC23T should be assigned to a novel species of the genus Lysinibacillus , for which the name Lysinibacillus acetophenoni sp. nov. is proposed. The type strain is strain JC23T ( = CCUG 57911T = KCTC 13605T = NBRC 105754T = DSM 23394T).

Lysinibacillus alkaliphilus sp. nov., an extremely alkaliphilic bacterium, and emended description of genus Lysinibacillus

A novel aerobic, alkaliphilic, Gram-staining-positive, endospore-forming bacterium, strain OMN17T, was isolated from a typical sandy loam soil under long-term OMN fertilization (half organic manure N plus half mineral N fertilizer) in northern China and was subjected to a polyphasic taxonomic study. The best growth was achieved at 30 °C and pH 8-10 in medium containing 0.5% (w/v) NaCl. The cell-wall peptidoglycan of strain OMN17T was type A4α; (l-Lys-Gly-d-Asp) and the cell-wall sugars were ribose, traces of galactose and arabinose. The only respiratory quinone found in strain OMN17T was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of strain OMN17T based on the 16S rRNA gene sequence showed that the strain was most closely related to Lysinibacillus halotolerans (97.8%), Lysinibacillus sinduriensis (97.5%), Lysinibacillus chungkukjangi (97.4%) and Lysinibacillus xylanilyticus (97.0%). The DNA-DNA hybridization results indicated that this strain was distinct from other species of the genus Lysinibacillus, the degree of relatedness being 21.8 ± 0.2% with L. halotolerans, 45.6 ± 1.8% with L. sinduriensis, 33.7 ± 1.2% with L. chungkukjangi and 23.7 ± 0.7% with L. xylanilyticus. The DNA G+C content of strain OMN17T was 38.1 mol%. The phenotypic, chemotaxonomic and genetic analyses identified strain OMN17T as a novel species of the genus Lysinibacillus, for which the name Lysinibacillus alkaliphilus sp. nov. is proposed. The type strain is OMN17T ( = DSM 28019T = CCTCC AB 2014073T). An emended description of the genus Lysinibacillus is also provided.

Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5

Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal polluted environments and biological control of Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus taxonomic group 1 that comprises mosquito pathogenic strains. After a combination assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60 contigs and 5,209 predicted-coding sequences) revealed strong functional and syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx), binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik, ars, czc, mnt, ter, cop, cad, and znu operons were identified.

Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0 and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T (99 % 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA–DNA relatedness between strain GY32T and L. sphaericus JCM 2502T were 81 % and 52 %, respectively. The G+C content of the genomic DNA of strain GY32T was 43.2 mol%. In addition, strain GY32T showed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA–DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T ( = NBRC 109424T = CGMCC 1.12212T = CCTCC M 2011307T).

Lysinibacillus fluoroglycofenilyticus sp. nov., a bacterium isolated from fluoroglycofen contaminated soil

A novel Gram-positive, fluoroglycofen-degrading bacterium, designated cmg86(T), was isolated from herbicide contaminated soil collected from Tongjing, Jiangsu province, China. Strain cmg86(T) was found to be aerobic, motile, endospore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain cmg86(T) belongs to the genus Lysinibacillus and showed the highest sequence similarity to Lysinibacillus meyeri DSM 25057(T) (97.9 %) and Lysinibacillus odysseyi KCTC 3961(T) (96.6 %). The cell-wall peptidoglycan type was determined to be A4α (L-Lys-D-Asp), which is consistent with the cell-wall characteristics of the genus Lysinibacillus. The predominant respiratory quinones were identified as menaquinone-7 (MK-7, 89.5 %) and meanaquinone-6 (MK-6, 8.9 %), and the major fatty acids were identified as iso-C15:0, anteiso-C15:0 and antesio-C17:0. The major polar lipids were found to be phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content of strain cmg86(T) was determined to be 37.6 mol%. The results of this study support the conclusion that strain cmg86(T) represents a novel species of the genus Lysinibacillus for which the name and Lysinibacillus fluoroglycofenilyticus sp. nov. is proposed. The type strain is cmg86(T) (=KCTC 33183(T) = CCTCC AB 2013247(T)).

Lysinibacillus halotolerans sp. nov., isolated from saline-alkaline soil

A novel aerobic, halotolerant bacterium, designated strain LAM612(T), was isolated from saline-alkaline soil samples from Lingxian County, Shandong Province, China. Cells of strain LAM612(T) were Gram-reaction-positive, endospore-forming, motile and rod-shaped. The optimal temperature and pH for growth were 35 °C and pH 6.0, respectively. Strain LAM612(T) could grow in the presence of up to 10% (w/v) NaCl. The genomic DNA G+C conten was 36.4 mol% as detected by the T(m) method. Comparative analysis of 16S rRNA gene sequences revealed that LAM612(T) was closely related to Lysinibacillus sinduriensis KACC 16611(T) (98.0%), L. chungkukjangi KACC 16626(T) (97.5%), L. massiliensis KCTC 13178(T) (97.4%), L. xylanilyticus KACC 15113(T) (97.2%), L. macroides DSM 54(T) (97.0%) and L. manganicus DSM 26584(T) (96.5%). The DNA-DNA hybridization values between strain LAM612(T) and its closest relatives ranged from 20.6% to 41.9%. The major fatty acids of strain LAM612(T) were iso-C(15 : 0) (40.8%), iso-C(16 : 0) (15.2%) and anteiso-C(15 : 0) (10.8%). The cell-wall peptidoglycan content was A4α (L-Lys-D-Asp). The predominant menaquinone was MK-7 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, five unknown glycolipids and an unknown lipid. Based on the DNA-DNA hybridization results and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM612(T) could be distinguished from the recognized species of the genus Lysinibacillus, and was suggested to represent a novel species of this genus, for which the name Lysinibacillus halotolerans sp. nov. is proposed. The type strain is LAM612(T) ( = ACCC 00718(T) = JCM 19611(T)).

Bacillus pakistanensis sp. nov., a halotolerant bacterium isolated from salt mines of the Karak Area in Pakistan

A rod shaped, non-motile, endospore forming, Gram-stain positive and moderately halotolerant strain, designated as NCCP-168(T), was isolated from salt mines sampled in the Karak district of Khyber Pakhtunkhwa Province in Pakistan. To delineate its taxonomic position, the strain was subjected to polyphasic characterization. Cells of strain NCCP-168(T) can grow at 10-40 (○)C (optimum at 30-35 (○)C), in a pH range of 5.0-9.0 (optimum at pH 8.0) and in 0-17 % (w/v) NaCl on agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NCCP-168(T) belongs to the genus Bacillus with the highest similarity to Bacillus seohaeanensis BH724(T) (97.1 %), and less than 97 % similarity with other closely related taxa (95.6 % with B. subtilis subsp. subtilis NCIB3610(T)). DNA-DNA relatedness between strain NCCP-168(T) and the type strains of closely related species was lower than 30 %. Chemotaxonomic data (major menaquinone, MK-7; cell wall peptidoglycan type, A1γ [meso-diaminopimelic acid]; major fatty acids, iso-C15:0 29.9 %, anteiso-C15:0 29.3 %, iso-C16:0 11.4 %, iso-C14:0 8.9 % and anteiso-C17:0 7.0 %; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine) support the affiliation of strain NCCP-168(T) with genus Bacillus. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NCCP-168(T) can be distinguished from the closely related taxa and thus represents a novel species in the genus Bacillus, for which the name Bacillus pakistanensis sp. nov. is proposed, with the type strain NCCP-168(T) (= KCTC 13786(T) = DSM 24834(T) = JCM 18975(T)).

Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31

Lysinibacillus sphaericus strain OT4b.31 is a native Colombian strain having no larvicidal activity against Culex quinquefasciatus and is widely applied in the bioremediation of heavy-metal polluted environments. Strain OT4b.31 was placed between DNA homology groups III and IV. By gap-filling and alignment steps, we propose a 4,096,672 bp chromosomal scaffold. The whole genome (consisting of 4,856,302 bp long, 94 contigs and 4,846 predicted protein-coding sequences) revealed differences in comparison to the L. sphaericus C3-41 genome, such as syntenial relationships, prophages and putative mosquitocidal toxins. Sphaericolysin B354, the coleopteran toxin Sip1A and heavy metal resistance clusters from nik, ars, czc, cop, chr, czr and cad operons were identified. Lysinibacillus sphaericus OT4b.31 has applications not only in bioremediation efforts, but also in the biological control of agricultural pests.

Lysinibacillus manganicus sp. nov., isolated from manganese mining soil

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were Lysinibacillus massiliensis CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), L. xylanilyticus XDB9T (96.7 %), L. sinduriensis JCM 15800T (96.2 %), L. odysseyi NBRC 100172T (95.9 %) and L. boronitolerans NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of L. massiliensis and L. sinduriensis were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).

Lysinibacillus contaminans sp. nov., isolated from surface water

A Gram-positive-staining, aerobic, endospore-forming bacterium, isolated as a contamination from an enrichment of enteric bacteria from surface water, was studied using a polyphasic taxonomic approach. 16S rRNA gene sequence similarity comparisons revealed that strain FSt3AT was grouped in the genus Lysinibacillus , most closely related to Lysinibacillus xylanilyticus XDB9T (98.1 %), Lysinibacillus parviboronicapiens BAM-582T and Lysinibacillus sphaericus DSM 28T (both 98.0 %). The 16S rRNA gene sequence similarity to other species of the genus Lysinibacillus was <97.5 %. The allocation to the genus Lysinibacillus was supported by a detailed chemotaxonomic characterization revealing a cell wall containing alanine, glutamic acid, aspartic acid and the diagnostic diamino acid lysine in a molar ratio of 1.6 : 1 : 0.9 : 0.8 (peptidoglycan type A4α), the major menaquinones MK-7 and MK-6, and polar lipids consisting of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unknown phospholipids, one unknown aminophospholipid and one unidentified aminolipid. The major fatty acids were iso- and anteiso-branched fatty acids. DNA–DNA hybridizations with the type strains of the most closely related species, L. parviboronicapiens DSM 25242T, L. xylanilyticus DSM 23493T and L. sphaericus DSM 28T, in addition to the results of physiological and biochemical tests, allowed genotypic and phenotypic differentiation of strain FSt3AT from these related species. Thus, FSt3AT represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus contaminans sp. nov. is proposed, with FSt3AT ( = CCM 8383T = DSM 25560T = CIP 110362T) as the type strain.

Lysinibacillus tabacifolii sp. nov., a novel endophytic bacterium isolated from Nicotiana tabacum leaves

A Gram-positive, catalase- and oxidase-positive, strictly aerobic, endospore-forming rod bacterium, designated K3514(T), was isolated from the leaves of Nicotiana tabacum. The strain was able to grow at temperatures of 8-40°C, pH 5.0-10.0 and NaCl concentrations of 0-7%. The predominant quinones (>30%) of this strain were MK-7(H2) and MK-7. Phylogenetic analysis of 16S rRNA gene sequence showed that strain K3514(T) was affiliated to the genus Lysinibacillus, with its closest relatives being Lysinibacillus mangiferihumi (98.3% sequence similarity), Lysinibacillus sphaericus (97.9% sequence similarity), Lysinibacillus fusiformis (97.4% sequence similarity), and Lysinibacillus xylanilyticus (97.3% sequence similarity). However, low levels of DNA-DNA relatedness values suggested that the isolate was distinct from the other closest Lysinibacillus species. Additionally, based on analysis of morphological, physiological, and biochemical characteristics, the isolate could be differentiated from the closest known relatives. Therefore, based on polyphasic taxonomic data, the novel isolate likely represents a novel species, for which the name Lysinibacillus tabacifolii sp. nov. and the type strain K3514(T) (=KCTC 33042(T) =CCTCC AB 2012050(T)) are proposed.

Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food

One bacterial strain 2RL3-2(T) was isolated from Chungkukjang, a traditional Korean fermented food made from soybeans, and determined to be a Gram-positive, aerobic, spore-forming rod. Growth of the novel strain was optimal at 30°C and pH 7.0. The 16S rRNA gene of strain 2RL3-2(T) showed the highest level of sequence similarity to Lysinibacillus sinduriensis BLB-1(T) (99.0%), Lysinibacillus massiliensis 4400831(T) (97.1%), Lysinibacillus xylanilyticus XDB9(T) (97.0%), and Lysinibacillus odysseyi 34hs-1(T) (96.8%). Phylogenetic analysis showed that strain 2RL3-2(T) formed a robust cluster with L. sinduriensis BLB-1(T), L. massiliensis 4400831(T), and L. odyssey 34hs-1(T). The major fatty acids were anteiso-C15:0 (47.3%), iso-C16:0 (16.3%), and anteiso-C17:0 (11.3%), and the only menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, along with an unknown phospholipid and two unknown lipids. The peptidoglycan type was A4α, with an interpeptide bridge of l-Lys-d-Asp. DNA-DNA hybridization values between strain 2RL3-2(T) and closely related Lysinibacillus species were below 43±4%. Therefore, based on phenotypic, chemotaxonomic, and phylogenetic characteristics, it was determined that strain 2RL3-2(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus chungkukjangi sp. nov. is proposed. The type strain is 2RL3-2(T) (=KACC 16626(T) =NBRC 108948(T)).

Lysinibacillus meyeri sp. nov., isolated from a medical practice

A Gram-positive, oxidase- and catalase-positive, strictly aerobic and motile bacterium, designated WS 4626T, was isolated from a medical practice. Spherical endospores were formed terminally in swollen rods. The genomic DNA G+C content was 37.1 mol%. Cells contained iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω10c, anteiso-C17 : 0 and iso-C17 : 0 as the predominant cellular fatty acids and MK-7 and MK-6 as the major isoprenoid quinones. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, the cell-wall peptidoglycan was type A4α, l-Lys-d-Asp and the major cell-wall sugar was xylose. The closest phylogenetic relatives were Lysinibacillus xylanilyticus XDB9T (96.7 % 16S rRNA gene sequence similarity) and Lysinibacillus odysseyi 34hs-1T (96.5 %). DNA–DNA relatedness between the isolate and L. odysseyi DSM 18869T was very low (6 %). On the basis of the data presented, strain WS 4626T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus meyeri sp. nov. is proposed. The type strain is WS 4626T ( = DSM 25057T = LMG 26643T).