Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis

Janibacter alittae sp. nov., an actinobacterium isolated from the gut of marine sandworm (Alitta virens)

A novel Gram-stain-positive, facultatively anaerobic, non-motile, catalase-positive, oxidase-negative and ovoid cocci, designated as A1S7T, was isolated from the gut of a marine sandworm (Alitta virens). Strain A1S7T exhibited optimal growth at temperatures of 20-30 ℃, pH 6-8 and in the presence of 2-4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain A1S7T belonged to the genus Janibacter, exhibiting a similarity of 99.0% to Janibacter cremeus KCTC 49873T, followed by Janibacter anophelis KCTC 19282T (98.8%), Janibacter hoylei KCTC 49872T (98.4%), Janibacter limosus KACC 20518T (98.2%) and Janibacter corallicola KACC 21120T (97.2%). The complete genome sequence of strain A1S7T revealed a genome size of 3360920 bp with a genomic G+C content of 70.1 mol%. The orthologous average nucleotide identity and the digital DNA-DNA hybridization values between strain A1S7T and Janibacter cremeus KCTC 49873T were determined to be 89.5 and 37.2%, respectively. The major respiratory quinone was MK-8(H4). The predominant fatty acids (>10%) included iso-C16:0, C17:1  ω8c, C18:1  ω9c and C17:0. Polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and three unknown polar lipids. The cell-wall peptidoglycan type was A1γ. The major whole-cell sugars were ribose, mannose and glucose. Based on phenotypic, phylogenetic, genotypic and chemotaxonomic properties, strain A1S7T represents a novel species in the genus Janibacter, for which the name Janibacter alittae sp. nov. is proposed. The type strain is A1S7T (=KCTC 49714T = JCM 36706T).

Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains

Introduction

Janibacter caused bacteriemia is one of the rare infections.

Methods

In the present study, we report the first isolation of Janibacter, a rare bacterial infection, from a bacteremia patient in China. Its 16S rDNA was amplified and designated as Janibacter YFY001, which belongs to J. indicus. In addition, its genome was sequenced through combined second- and third-generation genome sequencing methods.

Results

Based on its genome, we identified many virulence factors, such as catalase, gelatinase, FbpABC systems, and resistant genes, among others. Interestingly, three genomic islands were found in YFY001 by comparing its genome to environmental Janibacter strains.

Discussion

Our study not only provides the necessary genomic information for in-depth study of Janibacter, but also provides a novel methodology for studying future cases of rare bacterial infection.

Complete genome sequence of Janibaecter indicus YB324 from an Atlantic marine sediment

Janibacter indicus YB324, a gram-positive, aerobic and non-motile actinobacterium isolated from south Atlantic sediment at a depth of 2875 m. The complete genome sequence of the strain YB324 was obtained using PacBio Sequel HGAP.4 and comprised of 3,369,845 base pairs with a 71.3 mol% G + C content, 3225 protein-coding genes, 53 RNAs. In silico analysis confirmed the genes associated with polysaccharide hydrolyzation, nitrite reduction, and phenol degradation. Multiple natural product biosynthesis gene clusters were identified as well. The complete genome sequence will provide insight into the potential use of this strain in biotechnological and natural product biosynthesis applications.

Bacterial Microbiome in Wild-Caught Anopheles Mosquitoes in Western Thailand

Among the complex microbial community living in the mosquito midgut, some bacteria (e.g., Enterobacter spp.) can deliver effector molecules with anti-Plasmodium effects suppressing the development of malaria parasites (Plasmodium falciparum) before the öokinete can penetrate the mosquito midgut epithelium. Despite knowledge of this phenomenon, only a few studies have defined the diversity of microbiota in wild-caught adult Anopheles species. The objective of this study was to analyze and compare the bacterial microbiota in different Anopheles species, including representatives of the primary malaria vectors in western Thailand. Wild female Anopheles species were sampled from malaria-endemic areas in Tak and Mae Hong Son provinces near the Thai-Myanmar border. Midgut/abdominal bacterial diversity was assessed by examining the 16S rRNA gene, V3 hypervariable region, using PCR-Temporal Temperature Gel Electrophoresis (PCR-TTGE) profiling and sequence analysis. A total of 24 bacterial genera were identified from eight Anopheles species. Five bacterial genera were newly reported in Anopheles mosquitoes (Ferrimonas, Megasphaera, Pectobacterium, Shimwellia, and Trabulsiella). Five genera, including Megasphaera, were detected exclusively in a single-malaria (Plasmodium vivax) infected Anopheles minimus and not observed in other non-infected mosquitoes. The use of PCR-TTGE provides the first characterization of the midgut bacterial microbiome present in wild adult Anopheles in Thailand. Evidence that microbiota might impact pathogen development (suppression) in Anopheles and thereby reduce the risk of pathogen transmission deserves more studies to describe the presence and better understand the biological role of bacteria in natural mosquito populations.

Ecological and Ontogenetic Components of Larval Lake Sturgeon Gut Microbiota Assembly, Successional Dynamics, and Ecological Evaluation of Neutral Community Processes

Gastrointestinal (GI) or gut microbiotas play essential roles in host development and physiology. These roles are influenced partly by the microbial community composition. During early developmental stages, the ecological processes underlying the assembly and successional changes in host GI community composition are influenced by numerous factors, including dispersal from the surrounding environment, age-dependent changes in the gut environment, and changes in dietary regimes. However, the relative importance of these factors to the gut microbiota is not well understood. We examined the effects of environmental (diet and water sources) and host early ontogenetic development on the diversity of and the compositional changes in the gut microbiota of a primitive teleost fish, the lake sturgeon (Acipenser fulvescens), based on massively parallel sequencing of the 16S rRNA gene. Fish larvae were raised in environments that differed in water source (stream versus filtered groundwater) and diet (supplemented versus nonsupplemented Artemia fish). We quantified the gut microbial community structure at three stages (prefeeding and 1 and 2 weeks after exogenous feeding began). The diversity declined and the community composition differed significantly among stages; however, only modest differences associated with dietary or water source treatments were documented. Many taxa present in the gut were over- or underrepresented relative to neutral expectations in each sampling period. The findings indicate dynamic relationships between the gut microbiota composition and host gastrointestinal physiology, with comparatively smaller influences being associated with the rearing environments. Neutral models of community assembly could not be rejected, but selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for sturgeon conservation and aquaculture production specifically and applications of microbe-based management in teleost fish generally.IMPORTANCE We quantified the effects of environment (diet and water sources) and host early ontogenetic development on the diversity of and compositional changes in gut microbial communities based on massively parallel sequencing of the 16S rRNA genes from the GI tracts of larval lake sturgeon (Acipenser fulvescens). The gut microbial community diversity declined and the community composition differed significantly among ontogenetic stages; however, only modest differences associated with dietary or water source treatments were documented. Selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for lake sturgeon and early larval ecology and survival in their natural habitat and for conservation and aquaculture production specifically, as well as applications of microbe-based management in teleost fish generally.

Complete Genome Sequence of Janibacter melonis M714, a Janus-Faced Bacterium with Both Human Health Impact and Industrial Applications

Janibacter, a member of the Intrasporangiaceae family of Actinobacteria, is a Janus-faced bacterium that has both antibiotic resistance/pathogenicity and the ability to degrade pollutants, with significant research value. Here, we isolated the novel strain Janibacter melonis M714 from an irradiated area in Xinjiang Uygur Autonomous Region, China. J. melonis M714 contains one circular chromosome of 3,426,637 bp with a GC content of 72.98% and one plasmid of 54,436 bp with a GC content of 67.80%. The genome of J. melonis M714 contains 2,859 CDSs, 47 tRNA genes, and 6 rRNA genes. Genome assembly and annotation indicated that strain M714 has a high GC content and contains multiple notable functional genes, including a beta-lactam resistance gene and dioxygenase gene, which may be the key determinants of the strain's antibiotic resistance and xenobiotic degradation ability, respectively. The whole genome sequences of J. melonis M714 provide information that is useful for its potential applications in the degradation of pollutants and environmental remediation.

Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis

Strain Marseille-P4121^T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121^T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480^T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C_18:1ω9 (34.4%), C_16:0 (30.1%), and C_18:0 (19%). The draft genome size of strain Marseille-P4121^T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121^T (= CECT 9671^T = CSUR P4121^T) is the type strain of the new species Janibacter massiliensis sp. nov.

First case of bacteremia caused by Janibacter hoylei

Janibacter hoylei has previously been isolated only from an air sample in the upper atmosphere and clinical significance of J. hoylei was not yet established. Herein, we report a case of bacteremia caused by J. hoylei. An 8-week-old previously healthy male infant presented to the emergency room with fever. Blood culture yielded growth of Gram-positive bacilli and this microorganism could not be identified with conventional phenotypic methods. The isolate was identified by 16S rRNA gene sequencing, and the patient was successfully treated with vancomycin. To our knowledge, this is the first report of the recovery of J. hoylei in humans. This case shows that J. hoylei can be a potential pathogen in young children.

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam

The naturally acquired microbiota of Anopheles can influence vector’s susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles, especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria, Firmicutes, and Actinobacteria. Staphylococcus, Clostridium, and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles-associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon–Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in <30% of the specimens. Consequently, the core microbiota share by Anopheles from Binh Phuoc was very narrow, suggesting that Anopheles microbiota was greatly influenced by local environments. The repertory of bacterial genera in two specimens of An. dirus and An. pampanai naturally infected by Plasmodium vivax was also described as preliminary results. Finally, this study completed the repertory of bacteria associated to wild Anopheles. Anopheles associated-bacteria appeared specimen-dependent rather than mosquitoe species- or group-dependent. Their origin and the existence of Anopheles-specific bacterial taxa are discussed.

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam

The naturally acquired microbiota of Anopheles can influence vector's susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles, especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria, Firmicutes, and Actinobacteria. Staphylococcus, Clostridium, and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles-associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon-Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in <30% of the specimens. Consequently, the core microbiota share by Anopheles from Binh Phuoc was very narrow, suggesting that Anopheles microbiota was greatly influenced by local environments. The repertory of bacterial genera in two specimens of An. dirus and An. pampanai naturally infected by Plasmodium vivax was also described as preliminary results. Finally, this study completed the repertory of bacteria associated to wild Anopheles. Anopheles associated-bacteria appeared specimen-dependent rather than mosquitoe species- or group-dependent. Their origin and the existence of Anopheles-specific bacterial taxa are discussed.

Monashia flava gen. nov., sp. nov., an actinobacterium of the family Intrasporangiaceae

A novel actinobacterial strain, MUSC 78^T, was isolated from a mangrove soil collected from Peninsular Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 78^T represented a novel lineage within the class Actinobacteria. Strain MUSC 78^T formed a distinct clade in the family Intrasporangiaceae and was related most closely to members of the genera Terrabacter (98.3-96.8 % 16S rRNA gene sequence similarity), Intrasporangium (98.2-96.8 %), Humibacillus (97.2 %), Janibacter (97.0-95.3 %), Terracoccus (96.8 %), Kribbia (96.6 %), Phycicoccus (96.2-94.7 %), Knoellia (96.1-94.8 %), Tetrasphaera (96.0-94.9 %) and Lapillicoccus (95.9 %). Cells were irregular rod-shaped or cocci and stained Gram-positive. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid as the diagnostic diamino acid. The main cell-wall sugar was mannose and lower amounts of galactose and rhamnose were present. The predominant menaquinone was MK-8(H₄). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, diphosphatidylglycerol and phosphoglycolipid. The predominant fatty acids were iso-C_15 : 0, anteiso-C_15 : 0 and iso-C_16 : 0. The DNA G+C content was 73.1 mol%. Based on this polyphasic study, MUSC 78^T exhibited phylogenetic and phenotypic differences from members of the genera of the family Intrasporangiaceae, and therefore a novel species of a new genus, Monashia flava gen. nov., sp. nov., is proposed. The type strain of Monashia flava is MUSC 78^T ( = DSM 29621^T = MCCC 1K00454^T = NBRC 110749^T).

Pentachlorophenol degradation by Janibacter sp., a new actinobacterium isolated from saline sediment of arid land

Many pentachlorophenol- (PCP-) contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, and high salt concentrations. PCP-degrading microorganisms, adapted to grow and prosper in these environments, play an important role in the biological treatment of polluted extreme habitats. A PCP-degrading bacterium was isolated and characterized from arid and saline soil in southern Tunisia and was enriched in mineral salts medium supplemented with PCP as source of carbon and energy. Based on 16S rRNA coding gene sequence analysis, the strain FAS23 was identified as Janibacter sp. As revealed by high performance liquid chromatography (HPLC) analysis, FAS23 strain was found to be efficient for PCP removal in the presence of 1% of glucose. The conditions of growth and PCP removal by FAS23 strain were found to be optimal in neutral pH and at a temperature of 30 °C. Moreover, this strain was found to be halotolerant at a range of 1-10% of NaCl and able to degrade PCP at a concentration up to 300 mg/L, while the addition of nonionic surfactant (Tween 80) enhanced the PCP removal capacity.

Janibacter indicus sp. nov., isolated from hydrothermal sediment of the Indian Ocean

A Gram-staining-positive, aerobic and non-motile strain, 0704P10-1T, was isolated from hydrothermal sediment of the Indian Ocean. Phylogenetic, phenotypic and chemotaxonomic data for the organism supported that it belonged to the genus Janibacter . Strain 0704P10-1T showed 97.2–98.7 % 16S rRNA gene sequence similarities to the type strains of recognized members of the genus Janibacter . It contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall. MK-8(H4) was the only menaquinone detected. The major fatty acids were iso-C16 : 0, C17 : 1ω8c and 10-methyl C17 : 0. Meanwhile, the results of DNA–DNA hybridization studies and other physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 0704P10-1T from closely related species. Thus, strain 0704P10-1T represents a novel species of the genus Janibacter , for which the name Janibacter indicus sp. nov. is proposed. The type strain is 0704P10-1T ( = LMG 27493T = CGMCC 1.12511T).

Janibacter cremeus sp. nov., an actinobacterium isolated from sea sediment

A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus Janibacter , with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus Janibacter . Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus Janibacter . Therefore, strain HR08-44T represents a novel species of the genus Janibacter , for which the name Janibacter cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).

Genome sequence of Janibacter hoylei MTCC8307, isolated from the stratospheric air

Janibacter hoylei MTCC8307 was isolated from stratospheric air at an altitude of 41.4 km over Hyderabad, India. Here, we present the draft genome of Janibacter hoylei MTCC8307, which contains 3,139,099 bp with a G+C content of 72.8 mol%, 2,972 protein-coding genes, and 57 structural RNAs.

Symbiotic control of mosquito borne disease

It is well accepted that the symbiotic relationships insects have established with several microorganisms have had a key role in their evolutionary success. Bacterial symbiosis is also prevalent in insects that are efficient disease vectors, and numerous studies have sought to decrypt the basic mechanisms of the host-symbiont relationships and develop ways to control vector borne diseases. 'Symbiotic control', a new multifaceted approach that uses symbiotic microorganisms to control insect pests or reduce vector competence, seems particularly promising. Three such approaches currently at the cutting edge are: (1) the disruption of microbial symbionts required by insect pests; (2) the manipulation of symbionts that can express anti-pathogen molecules within the host; and (3) the introduction of endogenous microbes that affect life-span and vector capacity of the new hosts in insect populations. This work reviews current knowledge on microbial symbiosis in mosquitoes that holds promise for development of symbiotic control for mosquito borne diseases.

Mosquito/microbiota interactions: from complex relationships to biotechnological perspectives

To date around 3500 different species of mosquito have been described, several tens of which are vectors of pathogens of remarkable interest in public health. Mosquitoes are present all around the world showing a great ability to adapt to very different types of habitats where they play relevant ecological roles. It is very likely that components of the mosquito microbiota have given the mosquito a great capacity to adapt to different environments. Current advances in understanding the mosquito-microbiota relationships may have a great impact in a better understanding of some traits of mosquito biology and in the development of innovative mosquito-borne disease-control strategies aimed to reduce mosquito vectorial capacity and/or inhibiting pathogen transmission.

Knoellia flava sp. nov., isolated from pig manure

A Gram-positive, aerobic, non-spore-forming actinobacterial strain, designated strain TL1T, was isolated from pig manure in Wuhan, China. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H4). The major fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TL1T was most closely related to the type strains of Knoellia sinensis (98.5 %), Knoellia subterranea (98.2 %) and Knoellia aerolata (96.9 %). DNA–DNA relatedness values of strain TL1T with the type strains of K. sinensis and K. subterranea were 27.3 and 34.0 %, respectively. Comparison of phenotypic, chemotaxonomic and phylogenetic characteristics among strain TL1T and related organisms revealed that the isolate represents a novel species of the genus Knoellia, for which the name Knoellia flava sp. nov. is proposed; the type strain is TL1T ( = CGMCC 1.10749T = KCTC 19810T).

Ornithinibacter aureus gen. nov., sp. nov., a novel member of the family Intrasporangiaceae

A novel strain of the class Actinobacteria was isolated from a seawater sample collected in the South China Sea using modified R2A agar plates. The strain was a Gram-stain-positive, non-motile, non-spore-forming, catalase-positive, irregular rod-shaped bacterium. The strain grew at 4–45 °C and pH 5.0–10.2, and tolerated 5 % (w/v) NaCl. Based on its 16S rRNA gene sequence, the organism was related phylogenetically to members of the genera Fodinibacter (96.7 % similarity), Lapillicoccus (96.5 %), Knoellia (95.0–95.8 %), Oryzihumus (95.6 %) and Humibacillus (95.6 %). The cell-wall contained l-ornithine as the major diagnostic diamino acid in the peptidoglycan. MK-8(H4) was the predominant menaquinone. Major cellular fatty acids were iso-C18 : 1 ω9c, iso-C16 : 0, iso-C15 : 0 and C17 : 0. The G+C content of the DNA was 69.6 mol%. Phenotypic and phylogenetic data revealed that this strain represents a novel species in a new genus of the family Intrasporangiaceae, for which the name Ornithinibacter aureus gen. nov., sp. nov. is proposed; the type strain of Ornithinibacter aureus is HB09001T (=CGMCC 1.10341T =DSM 23364T).

Isolation and characterization of a newly isolated polycyclic aromatic hydrocarbons-degrading Janibacter anophelis strain JY11

The PAHs-degradation bacterium strain JY11 was newly isolated from the polluted soil in Jinan Oil Refinery Factory, Shandong Province of China. The isolate was identified as Janibacter anophelis with respect to its 16S rDNA sequence, DNA-DNA relatedness and fatty acid profiles, as well as various physiological characteristics. The strain was Gram-positive, non-motile, non-spore-forming, short rods in young culture, 0.8-1.0 microm in diameter and 1.3-1.6 microm long, and coccoid cells in the stationary phase of growth that are 1.0-1.2 microm in diameter and 1.3-1.5 microm long, occurred in pairs and sometimes in chains or in group, aerobic, oxidase-week positive, catalase-positive. J. anophelis strain JY11 can utilize naphthalene, phenanthrene, anthracene, pyrene, xylene, methanol, ethanol and salicylic acid as sole carbon source. The strain could remove 98.5% of phenanthrene, 82.1% of anthracene, and 97.7% of pyrene with an initial concentration of 500 ppm in five days without adding co-metabolism substrates and surfactants.

Fodinibacter luteus gen. nov., sp. nov., an actinobacterium isolated from a salt mine

A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2-96.0% similarity), Oryzihumus (95.6%), Terrabacter (94.9-95.4%), Janibacter (94.9-95.4%), Kribbia (95.0%), Lapillicoccus (95.0%) and Phycicoccus (94.2-95.0%) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18:1omega9c and C16:0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T=CCTCC AA 208036T) as the type strain of Fodinibacter luteus.

Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone

A novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the genera Tetrasphaera (94.6–97.1 % sequence similarity), Terrabacter (96.5 %), Knoellia (96.4 %), Terracoccus (96.4 %), Oryzihumus (96.4 %), Janibacter (96.1–96.4 %) and Intrasporangium (96.2 %). The chemotaxonomic results for the organism were as follows: ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1 ω8c and iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the family Intrasporangiaceae, for which the name Lapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T (=KCTC 19200T=DSM 18607T).

Janibacter corallicola sp. nov., isolated from coral in Palau

A novel Janibacter species is described on the basis of phenotypic, chemotaxonomic and genotypic data. Two bacterial strains were isolated in Palau, which were both Gram-positive, catalase-positive bacteria with meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The major menaquinone was MK-8(H(4)). Mycolic acids were not detected. The G+C content of the DNA was 70-71 mol%. Comparative 16S rDNA studies of the two isolated strains revealed that they both belonged to the genus Janibacter. DNA-DNA relatedness data revealed that 04PA2-Co5-61(T) and 02PA-Ca-009 belong to the same species, a new species of the genus Janibacter. From these results, Janibacter corallicola sp. nov. is proposed, with the type strain 04PA2-Co5-61(T) (=MBIC 08265(T), DSM 18906(T)).

Isolates of ‘Candidatus Nostocoida limicola’ Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp. nov., Tetrasphaera vanveenii sp. nov. and Tetrasphaera veronensis sp. nov

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium ‘Candidatus Nostocoida limicola’ and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S–23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA–DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that ‘Candidatus N. limicola’ strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74T=DSM 17519T=NCIMB 14128T), ‘Candidatus N. limicola’ strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70T=DSM 17518T=NCIMB 14127T) and ‘Candidatus N. limicola’ strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1T=DSM 17520T=NCIMB 14129T).

Kribbia dieselivorans gen. nov., sp. nov., a novel member of the family Intrasporangiaceae

Two Gram-positive, catalase-positive, irregular short rod- or coccoid-shaped bacterial strains, N113T and R33, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains N113T and R33 were representatives of the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains N113T and R33 form a lineage independent from those of members of the family Intrasporangiaceae. The novel isolates had cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and 10-methyl-C18 : 0, iso-C16 : 0, C18 : 1 ω9c, C16 : 0 and C18 : 0 as the major cellular fatty acids. The DNA G+C contents were 69.6–69.9 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the two novel strains from recognized members of the family Intrasporangiaceae. On the basis of phenotypic, phylogenetic and genetic data, strains N113T (=KCTC 19143T=JCM 13585T) and R33 are classified as representatives of a novel genus and species, Kribbia dieselivorans gen. nov., sp. nov., within the family Intrasporangiaceae.