Cellular Fatty Acid Composition Research Articles

Faecalibacterium taiwanense sp. nov., isolated from human faeces.

Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).

Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan.

Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.

Abstract 1711: Rearranged active enhancers and promoter-enhancer contacts promote lipid metabolic reprogramming during secondary trastuzumab adaptation of HER2 positive breast cancer

Abstract Background: The development of secondary trastuzumab resistance signifies an evolutionary adaptation within HER2-positive breast cancer during anti-HER2 treatment. Our research reveals a comprehensive metabolic reprogramming, with a particular emphasis on the synthesis of unsaturated fatty acids and the degradation of arachidonic acid, accompanying this adaptation. Non-mutational epigenetic variations, particularly alterations in active enhancers, coupled with the rearrangement of enhancer-promoter contacts, demonstrate robust correlations with lipid metabolic reprogramming. These findings suggest that non-mutational epigenetic variations play a crucial role in driving the adaptation to trastuzumab. Materials and Methods: In a prior investigation, we successfully generated secondary trastuzumab-resistant SKBR3_HR cells. In our current study, total RNA was extracted from both trastuzumab-resistant SKBR3_HR and trastuzumab-sensitive SKBR3 cells for transcriptome analysis. Additionally, mass spectrometry was employed to analyze cellular metabolism in both resistant and sensitive cell populations. Simultaneously, we utilized the CUT&Tag kit with an anti-H3K27ac antibody to create a sequencing library for active enhancer measurement. Furthermore, the Micro-C kit was applied to generate a sequencing library for genome contact measurement. Results: In our study, secondary trastuzumab-adaptive SKBR3_HR cells demonstrated a reduction in cellular unsaturated fatty acids, with more than 110 UFAs or UFA-containing lipids showing decreases, while only 36 exhibited increases. This phenomenon may be attributed to the downregulation of SCD, FADS2, and HACD2. Simultaneously, the upregulation of PTGS1 and PTGES may contribute to a higher conversion of arachidonic acid to prostaglandin E2 (PGE2), resulting in immune inhibition. In SKBR3 and SKBR3_HR cells, 10,955 and 10,889 non-promoter H3K27me3 peaks, respectively, were identified as active enhancer regions. Among them, 379 enhancers became silent, and 313 transitioned into an active state during the formation of trastuzumab adaptation. Trastuzumab adaptation led to an increase in intra-chromosomal interactions, particularly short-distance contacts (< 1MB). By employing the activity-by-contact (ABC) algorithm, we observed significant variant contacts between PTGES and SCD promoters and enhancers within 1MB genomic regions in SKBR3_HR cells compared to SKBR3 cells. Conclusion: The formation of secondary trastuzumab adaptation involves the rearrangement of active enhancers and promoter-enhancer contacts, serving as an effective force to drive lipid metabolic reprogramming, especially the synthesis of unsaturated fatty acids and PGE2 production, reshaping the cellular fatty acid composition and anti-tumor immunity. Citation Format: Ningjun Duan, Yijia Hua, Yongmei Yin. Rearranged active enhancers and promoter-enhancer contacts promote lipid metabolic reprogramming during secondary trastuzumab adaptation of HER2 positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1711.

Determination of double bond configuration of 2-hydroxy-fatty acids and emendation of cellular fatty acid composition of Aureispira marina and Aureispira maritima.

Aureispira marina is a marine bacterium with gliding motility isolated from the southern coastline of Thailand. It contained ceramide as a major cellular lipid composed of saturated or unsaturated branched chain 2-hydroxy-fatty acid and sphingosine. The structure of unsaturated 2-hydroxy-fatty acid was investigated in our previous study, but the geometric configuration of the double bond remained unclear. In the present study, 14-methyl-∆2-pentadecenol (∆2-iso-C16:1-ol) was prepared from D-2-hydroxy-15-methyl-∆3-hexadecenoic acid (D-2-OH-∆3-iso-C17:1) of the ceramide component, and analyzed by 1H and 13C NMR in comparison with ∆2-trans-hexadecenol (∆2-trans-n-C16:1-ol) derived from commercially available D-sphingosine. From the coupling constants of protons in the double bond and the chemical shift value of allylic carbon, the configuration of the double bond was determined as trans. Since the structure of 2-hydroxy-fatty acids was clarified, cellular fatty acids of A. marina and A. maritima, another species of the genus Aureispira, were reexamined, and the description on the cellular fatty acid composition of the genus Aureispira in the previous papers (Hosoya et al., 2006, Int. J. System. Evol. Microbiol., 56, 2931-2935; Hosoya et al., 2007, Int. J. System. Evol. Microbiol., 57, 1948-1951) lacking the description of 2-hydroxy-fatty acids was emended.

Pseudomonas solani sp. nov. isolated from the rhizosphere of eggplant in Japan.

The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006T, which was isolated from the rhizosphere of eggplant (Solanum melongena) growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006T represents a member of the genus Pseudomonas. The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. Phylogenetic analyses using the rpoD gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006T represents a member of the Pseudomonas resinovorans group; however, its phylogenetic position does not match that of any known species of the genus Pseudomonas. The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Pseudomonas tohonis TUM18999T (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006T represents a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas solani sp. nov., with Sm006T (= MAFF 212523T = ICMP 24689T) as the type strain.

Bombella pluederhausensis sp. nov., Bombella pollinis sp. nov., Bombella saccharophila sp. nov. and Bombella dulcis sp. nov., four Bombella species isolated from the environment of the western honey bee Apis mellifera.

Four strains of members of the genus Bombella were isolated from samples associated with the western honey bee Apis mellifera, which could not be assigned to a species with a validly published name. Strains TMW 2.2543T, TMW 2.2556T, TMW 2.2558T and TMW 2.2559T exhibit in silico DNA-DNA hybridisation (isDDH) and orthologous average nucleotide identity (orthoANI) values below species delineation thresholds compared with all described species of the genus Bombella and with each other. TMW 2.2556T and TMW 2.2558T form their own clade within the genus. The major respiratory quinone of all strains was Q-10. The composition of cellular fatty acids was diverse between strains. All strains stained Gram-negative, were rod-shaped, strictly aerobic, pellicle-forming, catalase-positive, oxidase-negative, mesophilic and grew over a wide pH range; they were halosensitive but glucose-tolerant. Unlike the other studied strains, TMW 2.2558T was non-motile. Phylogenetic, chemotaxonomic and physiological analyses revealed a clear distinction between all the strains and species with validly published names. All the data support the proposition of four novel species within the genus Bombella, namely Bombella pluederhausensis sp. nov., Bombella pollinis sp. nov., Bombella saccharophila sp. nov. and Bombella dulcis sp. nov., with the respective type strains Bombella pluederhausensis sp. nov. TMW 2.2543T (= DSM 114872T, = LMG 32791T), Bombella pollinis sp. nov. TMW 2.2556T (= DSM 114874T, = LMG 32792T), Bombella saccharophila sp. nov. TMW 2.2558T (= DSM 114875T, = LMG 32793T) and Bombella dulcis sp. nov. TMW 2.2559T (= DSM 114877T, = LMG 32794T). Moreover, three genomes available in the NCBI database that have not yet been described as species with validly published names could be assigned to the proposed species. Bombella sp. ESL0378 and Bombella sp. ESL0385 to Bombella pollinis sp. nov. and Bombella sp. AS1 to Bombella saccharophila sp. nov.

Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae.

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum Synergistota. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

Identification of key microRNAs regulating ELOVL6 and glioblastoma tumorigenesis

ELOVL fatty acid elongase 6 (ELOVL6) controls cellular fatty acid (FA) composition by catalyzing the elongation of palmitate (C16:0) to stearate (C18:0) and palmitoleate (C16:1n-7) to vaccinate (C18:1n-7). Although the transcriptional regulation of ELOVL6 has been well studied, the post-transcriptional regulation of ELOVL6 is not fully understood. Therefore, this study aims to evaluate the role of microRNAs (miRNAs) in regulating human ELOVL6. Bioinformatic analysis identified five putative miRNAs: miR-135b-5p, miR-135a-5p, miR-125a-5p, miR-125b-5p, and miR-22–3p, which potentially bind ELOVL6 3′-untranslated region (UTR). Results from dual-luciferase assays revealed that these miRNAs downregulate ELOVL6 by directly interacting with the 3′-UTR of ELOVL6 mRNA. Moreover, miR-135b-5p and miR-135a-5p suppress cell proliferation and migration in glioblastoma multiforme cells by inhibiting ELOVL6 at the mRNA and protein levels. Taken together, our results provide novel regulatory mechanisms for ELOVL6 at the post-transcriptional level and identify potential candidates for the treatment of patients with glioblastoma multiforme.

Penicillin Binding Protein 7/8 Is a Potential Drug Target in Carbapenem-Resistant Acinetobacter baumannii.

Limited therapeutic options dictate the need for new classes of antimicrobials active against carbapenem-resistant Acinetobacter baumannii. Presented data confirm and extend penicillin binding protein 7/8 (PBP 7/8) as a high-value target in the CR A. baumannii strain HUMC1. PBP 7/8 was essential for optimal growth/survival of HUMC1 in ex vivo human ascites and in a rat subcutaneous abscess model; in a mouse pneumonia model, the absence of PBP 7/8 decreased lethality 11-fold. The loss of PBP 7/8 resulted in increased permeability, sensitivity to complement, and lysozyme-mediated bactericidal activity. These changes did not appear to be due to alterations in the cellular fatty acid composition or capsule production. However, a decrease in lipid A and an increase in coccoidal cells and cell aggregation were noted. The compromise of the stringent permeability barrier in the PBP 7/8 mutant was reflected by an increased susceptibility to several antimicrobials. Importantly, expression of ampC was not significantly affected by the loss of PBP 7/8 and serial passage of the mutant strain in human ascites over 7 days did not yield revertants possessing a wild-type phenotype. In summary, these data and other features support PBP 7/8 as a high-value drug target for extensively drug-resistant and CR A. baumannii. Our results guide next-stage studies; the determination that the inactivation of PBP 7/8 results in an increased sensitivity to lysozyme enables the design of a high-throughput screening assay to identify small molecule compounds that can specifically inhibit PBP 7/8 activity.

Pseudomonas aegrilactucae sp. nov. and Pseudomonas morbosilactucae sp. nov., pathogens causing bacterial rot of lettuce in Japan.

Phytopathogenic bacterial strains (MAFF 301350T, MAFF 302030T and MAFF 302046), isolated from lettuce (Lactuca sativa var. capitata) with bacterial rot disease in Japan, were subjected to polyphasic characterization to determine their taxonomic affiliations. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with polar flagella and rod-shaped. The results of similarity searches and phylogenetic analyses based on the 16S rRNA gene sequences, as well as the analysis results of the cellular fatty acid composition and genomic DNA G+C content indicated that these strains belong to the genus Pseudomonas . Phylogenetic analyses using the rpoD gene sequences and phylogenomic analyses of the whole genome sequences grouped them into the Pseudomonas putida group (MAFF 301350T) and the Pseudomonas fluorescens group (MAFF 302030T and MAFF 302046), but the phylogenetic positions of the strains did not match those of any known Pseudomonas species. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were lower than the thresholds for prokaryotic species delineation (95–96 and 70 %, respectively). Phenotypic characteristics, pathogenicity toward lettuce, cellular fatty acid composition and whole-cell MALDI-TOF mass spectrometry profiles could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Pseudomonas , Pseudomonas aegrilactucae sp. nov. for MAFF 301350T and Pseudomonas morbosilactucae sp. nov. for MAFF 302030T and MAFF 302046. The respective type strains are MAFF 301350T (= ICMP 23989T) and MAFF 302030T (= ICMP 24377T).

Investigation of Immunostimulatory Effects of Heat-Treated Lactiplantibacillus plantarum LM1004 and Its Underlying Molecular Mechanism.

Postbiotics are defined as probiotics inactivated by heat, ultraviolet radiation, sonication, and other physical or chemical stresses. Postbiotics are more stable than probiotics, and these properties are advantageous for food additives and pharmacological agents. This study investigated the immunostimulatory effects of heat-treated Lactiplantibacillus plantarum LM1004 (HT-LM1004). Cellular fatty acid composition of L. plantarum LM1004 isolated form kimchi was analyzed by gas chromatography-mass spectrometry detection system. The nitric oxide (NO) content was estimated using Griess reagent. Immunostimulatory cytokines were evaluated using enzyme-linked immunosorbent assay. Relative protein expressions were evaluated by western blotting. Phagocytosis was measured using enzyme-labelled Escherichia coli particles. L. plantarum LM1004 showed 7 kinds of cellular fatty acids including palmitic acid (C16:0). The HT-LM1004 induced release of NO and upregulated the inducible NO synthase in RAW 264.7 macrophage cells. Tumor necrosis factor-α and interleukin-6 levels were also increased compared to control (non-treated macrophages). Furthermore, HT-LM1004 modulated mitogen-activated protein kinase (MAPK) subfamilies including p38 MAPK, extracellular signal-regulated kinase 1/2, and c-Jun N-terminal kinase. Therefore, these immunostimulatory effects were attributed to the production of transcriptional factors, such as nuclear factor kappa B (NF-κB) and the activator protein 1 family (AP-1). However, HT-LM1004 did not showed significant phagocytosis of RAW 264.7 macrophage cells. Overall, HT-LM1004 stimulated MAPK/AP-1 and NF-κB expression, resulting in the release of NO and cytokines. These results will contribute to the development of diverse types of food and pharmacological products for immunostimulatory agents with postbiotics.

Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan

Phytopathogenic bacterial strains (MAFF 311094T, MAFF 311095, MAFF 311096 and MAFF 311097), which were isolated from rot lesions of parsley (Petroselinum crispum) sampled in Miyagi, Japan, were subjected to polyphasic characterization to determine their taxonomic position. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. The 16S rRNA gene sequences analyses revealed that the strains belong to the genus Pseudomonas, exhibiting the highest sequence similarity to Pseudomonas sivasensis P7T (99.93% sequence similarity), Pseudomonas cyclaminis MAFF 301449T (99.93 %), Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas kitaguniensis MAFF 212408T (99.86 %) and Pseudomonas antarctica CMS 35T (99.79 %). The genomic DNA G+C content was 60.1 mol%, and the major cellular fatty acids (>5 % of the total fatty acids) were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c), summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C17:0 cyclo. The rpoD sequence-based phylogenetic and whole genome-based phylogenomic analyses demonstrated that the strains are a member of the Pseudomonas fluorescens subgroup, but their phylogenetic position does not match those of any members of this subgroup. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were ≤90.64% and ≤41.9 %, respectively, which were below the thresholds for prokaryotic species delineation (95-96 and 70%, respectively). Phenotypic characteristics, pathogenicity toward parsley and cellular fatty acid composition could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data presented in this study revealed that the strains constitute a novel Pseudomonas species, for which we propose the name Pseudomonas petroselini sp. nov., with MAFF 311094T (=ICMP 24279T) being the type strain.

Furfurilactobacillus milii sp. nov., isolated from fermented cereal foods.

Genomic characterization of Furfurilactobacillus rossiae revealed that strains which were previously identified as F. rossiae are genetically heterogeneous. The 16S rRNA gene sequences of strains FUA3430, FUA3583, C5, FUA3115 and FUA3119, were 99.6 % identical to F. rossiae but the core genome analysis revealed that these strains share less than 93 % average nucleotide identity (ANI) with the F. rossiae type strain DSM 15814T. Because the ANI value is below the threshold for delineation of bacterial species, we propose the novel species Furfurilactobacillus milii sp. nov. with the type strain FUA3430T (=DSM 113338T=LMG 32478T). Strains of F. milii have smaller genomes than F. rossiae, lack the pdu-cbi-cob-hem cluster which is responsible for 1,2-propanediol utilization in F. rossiae, and lack genes involved in ethanolamine utilization. Two strains of the novel species (FUA3430T and FUA3583) were compared to F. rossiae FUA3214. Analysis of the cellular fatty acid composition and metabolite analysis did not reveal significant differences between F. milii sp. nov. and F. rossiae FUA3124. Although the growth requirements with respect to temperature and pH were very similar, only the strain of F. rossiae utilized melibiose and d-xylose. Morphological differences were also seen in the colony and cell size of the novel compared to F. rossiae.

Role of Fatty Acid Elongase Elovl6 in the Regulation of Fatty Acid Quality and Lifestyle-related Diseases

The increasing prevalence of obesity worldwide has become an alarming public health concern because of dramatic increases in the incidence of obesity-associated diseases, including type 2 diabetes mellitus (T2DM). Peripheral insulin resistance and impaired insulin secretion remain the core defects in T2DM. Despite significant advances in unraveling the mechanisms underlying these defects, many of the metabolic pathways and regulators involved in insulin resistance and β-cell dysfunction are not completely understood. This review proposes that manipulating the fatty acid (FA) composition by blocking ELOVL fatty acid elongase 6 (Elovl6) could protect against insulin resistance, impaired insulin secretion, and obesity-related disorders. Elovl6 is a microsomal enzyme involved in the elongation of C16 saturated and monounsaturated FAs to form C18 FAs. We have reported that mice with Elovl6 deletion are protected against obesity-induced insulin resistance or β-cell failure because the cellular FA composition is changed, even with concurrent obesity. Therefore, Elovl6 appears to be a crucial metabolic checkpoint, and limiting the expression or activity of Elovl6 could be a new therapeutic approach in the treatment of T2DM.

Pseudomonas alliivorans sp. nov., a plant-pathogenic bacterium isolated from onion foliage in Georgia, USA

This study provides a taxonomic characterization of three bacterial strains isolated from onion seedlings in Georgia USA. Yellow-colored colonies were isolated, and a diffusible fluorescent pigment was visible under ultraviolet light on King’s medium B. Preliminary analysis of the basic phenotype tests and 16S rRNA gene sequence analysis indicated the onion strains were closely related to Pseudomonas viridiflava with the highest similarity to P. viridiflava DSM 6694T (99.6%). The phylogenomic analyses based on whole genome sequences showed that the onion strains formed a separate monophyletic clade from other species with P. viridiflava as the closest neighbor. When the onion strains and the P. viridiflava type strain were compared, the average nucleotide identity values was 91.6%. Additionally, the digital DNA–DNA hybridization values of the onion strains were 45.8% or less when compared to the type strains of their close relatives, including P. viridiflava. In addition, biochemical, physiological features, and cellular fatty acid compositions were determined for a polyphasic taxonomic analysis. The results supported that the three onion strains represented a novel Pseudomonas species. We propose a new species as Pseudomonas alliivorans sp. nov., with 20GA0068T (=LMG 32210T = CFBP 8885T) as the type strain. The DNA G + C content of the strain 20GA0068T is 59.1 mol%.

Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure.

ABSTRACTCulture-independent analysis shows that Legionella spp. inhabit a wide range of low-temperature environments, but to date, no psychrotolerant or psychrophilic strains have been reported. Here, we characterized the first cultivated psychrotolerant representative, designated strain TUM19329T, isolated from an Antarctic lake using a polyphasic approach and comparative genomic analysis. A genome-wide phylogenetic tree indicated that this strain was phylogenetically separate at the species level. Strain TUM19329T shared common physiological traits (e.g., Gram-negative, limited growth on buffered charcoal-yeast extract α-ketoglutarate [BCYEα] agar with l-cysteine requirements) with its relatives, but it also showed psychrotolerant growth properties (e.g., growth at 4°C to 25°C). Moreover, this strain altered its own cellular fatty acid composition to accumulate unsaturated fatty acid at a lower temperature, which may help maintain the cell membrane fluidity. Through comparative genomic analysis, we found that this strain possessed massive mobile genetic elements compared with other species, amounting to up to 17% of the total genes. The majority of the elements were the result of the spread of only a few insertion sequences (ISs), which were spread throughout the genome by a “copy-and-paste” mechanism. Furthermore, we found metabolic genes, such as fatty acid synthesis-related genes, acquired by horizontal gene transfer (HGT). The expansion of ISs and HGT events may play a major role in shaping the phenotype and physiology of this strain. On the basis of the features presented here, we propose a new species—Legionella antarctica sp. nov.—represented by strain TUM19329T (= GTC 22699T = NCTC 14581T).IMPORTANCE This study characterized a unique cultivated representative of the genus Legionella isolated from an Antarctic lake. This psychrotolerant strain had some common properties of known Legionella species but also displayed other characteristics, such as plasticity in fatty acid composition and an enrichment of mobile genes in the genome. These remarkable properties, as well as other factors, may contribute to cold hardiness, and this first cultivated cold-tolerant strain of the genus Legionella may serve as a model bacterium for further studies. It is worth noting that environmentally derived 16S rRNA gene phylotypes closely related to the strain characterized here have been detected from diverse environments outside Antarctica, suggesting a wide distribution of psychrotolerant Legionella bacteria. Our culture- and genome-based findings may accelerate the ongoing studies of the behavior and pathogenicity of Legionella spp., which have been monitored for many years in the context of public health.

Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales)

We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.

Iodidimonas gelatinilytica sp. nov., aerobic iodide-oxidizing bacteria isolated from brine water and surface seawater.

Chemo-organotrophic iodide (I-)-oxidizing bacterial strains Hi-2T and Mie-1 were isolated from iodide-rich natural gas brine water in Chiba and surface seawater in Mie, Japan, respectively. Cells of strains Hi-2T and Mie-1 were aerobic, Gram-negative and rod-shaped (0.3-0.5µm width and 1.2-4.4µm in length). Two isolates grew optimally at 30°C, pH 7.5 and with 3% NaCl (w/v). Iodide oxidation to form molecular iodine (I2) was a biochemically unique trait for strains Hi-2T and Mie-1. The major cellular fatty acids are C18:1ω7c, C16:1ω5c and C18:1 2-OH. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that strains Hi-2T and Mie-1 were located near Iodidimonas muriae C-3T with 99.2% sequence similarity. The calculated digital DNA-DNA hybridization (dDDH) value of 65.7-65.9% between the two isolates and I. muriae C-3T was lower than the threshold of 70%, which was used for prokaryotic species delineation. Strains Hi-2T and Mie-1 differed in the hydrolysis of aesculin, the hydrolysis of gelatin and the major cellular fatty acids composition from I. muriae C-3T. Considering these biochemical properties, the major cellular fatty acids composition and dDDH value, a novel species is proposed for strains Hi-2T (= JCM 17844T = LMG 28661T) and Mie-1 (= JCM 17845 = LMG 28662), to be named Iodidimonas gelatinilytica.

Capillibacterium thermochitinicola gen. nov., sp. nov., a novel anaerobic thermophilic chitinolytic bacterium from compost.

A novel Gram-negative, spore forming, obligately anaerobic, thermophilic, chitin-degrading bacterium, designated UUS1-1T, was isolated from compost on Ishigaki Island, Japan by enrichment culturing using chitin powder as the carbon source. The strain has unique, long, hair-like rod morphological features and exhibits strong degradation activity toward crystalline chitin under thermophilic conditions. Growth of the novel strain was observed at 45–65 °C (optimum, 55 °C) and pH 6.5–7.5 (optimum, pH 7.0). In addition to chitin, the strain utilized several other carbon sources, including N-acetylglucosamine, glucose, galactose, mannose, maltose, cellobiose, fructose and sucrose. The end products of chitin degradation were acetate, lactate, H2 and CO2. Phylogenetic tree analysis based on 16S rRNA gene sequences revealed a clear affiliation of the proposed bacterium to the phylum Firmicutes; the most closely related species were Hydrogenispora ethanolica LX-BT and Desulfotomaculum thermobenzoicum DSM6193T with similarities of 90.4 and 87.8 %, respectively. The G+C content of the genomic DNA was 52.1 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of UUS1-1T and H. ethanolica LX-BT were 65.5 and 21.0 %, respectively. The cellular fatty acid composition of the strain was C16 : 0, anteiso-C15 : 0, C14 : 0, C12 : 0 3-OH and dimethyl acetal-C13 : 0. Based on phenotypic, chemotaxonomic and genotypic analysis, strain UUS1-1T represents a novel genus and species, for which the name Capillibacterium thermochitinicola gen. nov., sp. nov. is proposed. The type strain is UUS1-1T (=JCM 33882T=DSM 111537T).

Detection of 2-hydroxy-fatty acids and 2-hydroxy-fatty acid-containing ceramides in a gliding marine bacterium Aureispira marina.

The cellular fatty acid composition of Aureispira marina IAM 15389T (JCM 23197T), a gliding bacterium isolated from the coastline of Thailand, was re-examined by using a standard MIDI method based on alkaline hydrolysis, and two other methods. The direct transesterification using 5% HCl/methanol or 4 M HCl hydrolysis followed by methyl esterification revealed that 2-hydroxy-15-methyl-hexadecanoic acid (2-OH-iso-C17:0) and 2-hydroxy-15-methyl-hexadecenoic acid (2-OH-iso-C17:1), which were not reported in a previous paper, were found to be major cellular fatty acids of this bacterium, and the amount of 2-OH-iso-C17:1 was even higher than that of arachidonic acid (C20:4), a characteristic polyunsaturated fatty acid present in this bacterium. These 2-hydroxy-fatty acids were contained in two cellular lipids that were relatively stable against alkaline hydrolysis. One of them was analyzed by mass spectrometry, 1H-nuclear magnetic resonance, and other chemical methods, and identified as a ceramide composed of 2-hydroxy-fatty acid and sphingosine of 19 carbons with three double bonds. A minor ceramide containing 18 carbon sphingosine with three double bonds was also detected.