Search

Herein, we report a rare case of pulmonary nontuberculous mycobacterial (NTM) infection caused by Mycolicibacter kumamotonensis in a 73-year-old man successfully treated with clarithromycin, rifampicin, and ethambutol. Seven cases of NTM disease caused by M. kumamotonensis have been previously described, with characteristics differing from those of more common NTM diseases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Acetic acid bacteria - belonging to the Acetobacteraceae family - are found in the gut of many sugar-feeding insects. In this study, six strains have been isolated from the hemipteran leafhopper Euscelidius variegatus . While they exhibit high 16S rRNA gene sequence similarities to uncultured members of the Acetobacteraceae family, they could not be unequivocally assigned to any particular type species. Considering the clonality of the six isolates, the EV16P T strain was used as a representative of this group of isolates. The genome sequence of EV16P T is composed of a 2.388 Mbp chromosome, with a DNA G+C content of 57 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis indicate that EV16P T forms a monophyletic clade with the uncultivated endosymbiont of Diaphorina citri , the Candidatus Kirkpatrickella diaphorinae. Such a phylogenetic clade is positioned between those of Asaia-Swaminathania and Kozakia . The genomic distance metrics based on gene and protein sequences support the proposal that EV16P T is a new species belonging to a yet-undescribed genus. It is a rod-shaped Gram-stain-negative bacterium, strictly aerobic, non-motile, non-spore-forming, showing optimal growth without salt (NaCl) at 30 °C and pH of 6-7. The major quinone is Q10, and the dominant cellular fatty acids (>10%) are C 18:l ω 7c, C 19 : 0 cyclo ω 6c, C 16 : 0 and C 19 : 1 2OH. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, along with unidentified aminophospholipids, glycophospholipids, aminolipids and lipids. Based on a polyphasic approach, including phylogenetic, phylogenomic, genome relatedness, phenotypic and chemotaxonomic characterisations, EV16P T (= KCTC 8296 T , = DSM 117028 T ) is proposed as a representative of a novel species in a novel genus with the proposed name Sorlinia euscelidii gen. nov., sp. nov., in honour of Prof. Claudia Sorlini, an Italian environmental microbiologist at the University of Milan who inspired the research on microbial diversity, including symbiosis in plants and animals.

Strain NIBR12 T (=KACC 22094 T =HAMBI 3739 T ), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture ( Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12 T belongs to the genus Roseococcus , with its closest neighbours being Roseococcus suduntuyensis SHET T (98.8%), Roseococcus thiosulfatophilus RB-3 T (97.7%), " Sediminicoccus rosea" R-30 T (95.7 %) and Rubritepida flocculans H-8 T (95.0 %). Genomic comparison of strain NIBR12 T with type species in the genus Roseococcus was conducted using digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12 T was 70.9 mol%. The major fatty acids of strain NIBR12 T were summed feature 8 (C 18 : 1   ω 7 c and/or C 18:1 ω 6 c ) and summed feature 3 (C 16 : 1 ω 6 c /C 16 : 1 ω 7 c ). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12 T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12 T is identified as represeting a novel species of the genus Roseococcus , for which the name Roseococcus microcysteis sp. nov. is proposed.

Engineered living materials (ELMs) based on bacterial cellulose (BC) offer a promising avenue for cheap-to-produce materials that can be programmed with genetically encoded functionalities. Here we explore how ELMs can be fabricated in a modular fashion from millimetre-scale biofilm spheroids grown from shaking cultures of Komagataeibacter rhaeticus. Here we define a reproducible protocol to produce BC spheroids with the high yield bacterial cellulose producer K. rhaeticus and demonstrate for the first time their potential for their use as building blocks to grow ELMs in 3D shapes. Using genetically engineered K. rhaeticus, we produce functionalized BC spheroids and use these to make and grow patterned BC-based ELMs that signal within a material and can sense and report on chemical inputs. We also investigate the use of BC spheroids as a method to regenerate damaged BC materials and as a way to fuse together smaller material sections of cellulose and synthetic materials into a larger piece. This work improves our understanding of BC spheroid formation and showcases their great potential for fabricating, patterning and repairing ELMs based on the promising biomaterial of bacterial cellulose., (© 2021. The Author(s).)

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 T and T18 T , were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6 T and T18 T showed similarities with Belnapia rosea CGMCC 1.10758 T and Belnapia moabensis CP2C T (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6 T and T18 T , respectively; the average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia . The predominant fatty acids were summed feature 8 (C 18 : 1 ω7 c/ C 18 : 1 ω6 c ), C 16 : 0 , C 18 : 1 2-OH and summed feature 3 (C 16 : 1 ω7 c/ C 16 : 1 ω6 c ). According to he results of the polyphasic study, strains T6 T and T18 T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6 T = CECT 30228 T =DSM 112073 T ) and Belnapia arida sp. nov. (type strain T18 T =CECT 30229 T =DSM 112074 T ) are proposed, respectively.

To date, the production of bacterial nanocellulose (BNC) by standard methods has been well known, while the use of low-cost feedstock as an alternative medium still needs to be explored for BNC commercialization. This study explores the prospect for the use of the different aqueous extract of fruit peel wastes (aE-FPW) as a nutrient and carbon source for the production of BNC. Herein, this objective was accomplished by the use of a novel, high- yielding strain, isolated from rotten apple and further identified as Komagataeibacter xylinus IITR DKH20 using 16 s rRNA sequencing analysis. The physicochemical properties of BNC matrix collected from the various aE-FPW mediums were similar or advanced to those collected with the HS medium. Statistical optimization of BNC based on Central Composite Design was performed to study the effect of significant parameters and the results demonstrated that the BNC yield (11.44 g L -1 ) was increased by 4.5 fold after optimization., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The mosquito microbiota is composed of several lineages of microorganisms whose ecological roles and evolutionary histories have yet to be investigated in depth. Among these microorganisms, Asaia bacteria play a prominent role, given their abundance in the gut, reproductive organs, and salivary glands of different mosquito species, while their presence has also been reported in several other insects. Notably, Asaia has great potential as a tool for the control of mosquito-borne diseases. Here, we present a wide phylogenomic analysis of Asaia strains isolated from different species of mosquito vectors and from different populations of the Mediterranean fruit fly (medfly), Ceratitis capitata , an insect pest of worldwide economic importance. We show that phylogenetically distant lineages of Asaia experienced independent genome reductions, despite following a common pattern, characterized by the early loss of genes involved in genome stability. This result highlights the role of specific metabolic pathways in the symbiotic relationship between Asaia and the insect host. Finally, we discovered that all but one of the Asaia strains included in the study possess the pyrethroid hydrolase gene. Phylogenetic analysis revealed that this gene is ancestral in Asaia , strongly suggesting that it played a role in the establishment of the symbiotic association between these bacteria and the mosquito hosts. We propose that this gene from the symbiont contributed to initial pyrethroid resistance in insects harboring Asaia , also considering the widespread production of pyrethrins by several plants. IMPORTANCE We have studied genome reduction within several strains of the insect symbiont Asaia isolated from different species/strains of mosquito and medfly. Phylogenetically distant strains of Asaia , despite following a common pattern involving the loss of genes related to genome stability, have undergone independent genome reductions, highlighting the peculiar role of specific metabolic pathways in the symbiotic relationship between Asaia and its host. We also show that the pyrethroid hydrolase gene is present in all the Asaia strains isolated except for the South American malaria vector Anopheles darlingi , for which resistance to pyrethroids has never been reported, suggesting a possible involvement of Asaia in determining resistance to insecticides., (Copyright © 2021 Comandatore et al.)

Granulibacter bethesdensis can infect patients with chronic granulomatous disease, an immunodeficiency caused by reduced phagocyte NADPH oxidase function. Intact G. bethesdensis ( Gb ) is hypostimulatory compared to Escherichia coli , i.e., cytokine production in human blood requires 10-100 times more G. bethesdensis CFU/mL than E. coli . To better understand the pathogenicity of G. bethesdensis , we isolated its lipopolysaccharide ( Gb LPS) and characterized its lipid A. Unlike with typical Enterobacteriaceae , the release of presumptive Gb lipid A from its LPS required a strong acid. NMR and mass spectrometry demonstrated that the carbohydrate portion of the isolated glycolipid consists of α-Man p -(1→4)-β-Glc p N3N-(1→6)-α-Glc p N-(1⇿1)-α-Glc p A tetra-saccharide substituted with five acyl chains: the amide-linked N-3' 14:0(3-OH), N-2' 16:0(3-O16:0), and N-2 18:0(3-OH) and the ester-linked O-3 14:0(3-OH) and 16:0. The identification of glycero-d-talo-oct-2-ulosonic acid (Ko) as the first constituent of the core region of the LPS that is covalently attached to GlcpN3N of the lipid backbone may account for the acid resistance of Gb LPS. In addition, the presence of Ko and only five acyl chains may explain the >10-fold lower proinflammatory potency of Gb Ko-lipidA compared to E. coli lipid A, as measured by cytokine induction in human blood. These unusual structural properties of the G.bethesdensis Ko-lipid A glycolipid likely contribute to immune evasion during pathogenesis and resistance to antimicrobial peptides.

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880 T and TMW 2.1889 T ) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880 T are non-motile, thin/short rods, and cells of TMW 2.1889 T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella . Strain TMW 2.1880 T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880 T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889 T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889 T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C 16 : 0 , C 19 : 0 cyclo ω 8 c and summed feature 8, respectively, and additionally C 14 : 0 2-OH only for TMW 2.1880 T and C 14 : 0 only for TMW 2.1889 T . Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella , for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880 T (=LMG 31882 T =CECT 30114 T ) and TMW 2.1889 T (=LMG 31883 T =CECT 30113 T ).

Acid sulfate soil is found throughout Southeast Asia, and its strong acidity (pH 2-4) is accompanied by various plant growth-inhibiting factors that can reduce crop production. Among these factors, aluminum elution from the soil due to soil acidity strongly inhibits crop growth and is particularly problematic for agricultural production. We previously isolated Acidocella aluminiidurans strain AL46, a highly aluminum-tolerant bacterium, from the rhizospheres of the grass Panicum repens, inhabiting the acid sulfate soil in Vietnam. To elucidate the mechanism underlying the high aluminum tolerance of strain AL46, in the present study, we investigated the aluminum-adsorption ability of strain AL46 surface polysaccharides and confirmed the strong adsorption ability of the capsular polysaccharide (AL46CPS). Based on this finding, we further determined the chemical structure of AL46CPS using 1 H and 13 C NMR spectroscopy by conducting 2D DQF-COSY, TOCSY, HSQC, HMBC, and NOESY experiments. AL46CPS comprises a trisaccharide repeating unit with the following structure: [→2)-β-d-Rhap-(1 → 3)-α-d-Rhap-(1 → 2)-α-d-Rhap-(1→] n . These findings highlight the potential application of AL46CPS as a new aluminum-adsorbing substance in acidic environments to prevent crop loss., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

In this study, bacterial strains Ha5 T , Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15-37°C (optimum, 28-30°C) and in the presence of 0-1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C 18:1 ω7c, C 16:0 , C 19:0 ω8c cyclo, C 14:0 , and C 16:0 2-OH. Strains Ha5 T , Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56-94.63%) with Neokomagataea tanensis NBRC106556 T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5 T , Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteaceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5 T as the type strain.

Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569 T , were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569 T belong to the family Acetobacteraceae and the most closely related species are Gluconacetobacter takamatsuzukensis (96.1 %), Gluconacetobacter tumulisoli (95.9 %) and Gluconacetobacter sacchari (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569 T are clearly distinguished from other genera in the family Acetobacteraceae by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569 T do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569 T possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C 18 : 1  ω7 c and/or C 18 : 1  ω6 c ; 40.3-40.4 %), C 18 : 1 2OH (22.7-23.7 %) and summed feature 2 (C 14 : 0 3OH and/or C 16 : 1 iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569 T is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569 T from other genera in the family Acetobacteraceae supporting the proposal of Lichenicola gen. nov., with the type species Lichenicola cladoniae sp. nov. (type strain, PAMC 26569 T =KCCM 43315 T =JCM 33604 T ).

A Gram-stain-negative, strictly aerobic bacterium, designated strain PeD5 T , was isolated from a green alga Pediastrum duplex from the Nakdong river of the Republic of Korea. Cells were non-motile cocci, catalase-negative and oxidase-positive. Growth of PeD5 T was observed at 25-40 °C (optimum, 35 °C) and pH 5.0-10.0 (optimum, pH 7-8), and in the presence of 0-0.25% (w/v) NaCl (optimum, 0%). PeD5 T contained C 16:0 , C 18:1 ω7 c 11-methyl, summed feature 3 (comprising C 16:1 ω7 c and/or C 16:1 ω6 c ) and summed feature 8 (comprising C 18:1 ω7 c and/or C 18:1 ω6 c ) as major cellular fatty acids (>5%) and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified aminolipid were detected as major polar lipids. The genomic DNA G+C content of PeD5 T was 71.0 mol%. PeD5 T was most closely related to Roseomonas stagni HS-69 T with a 97.6% 16S rRNA sequence similarity and shared less than 96.3% 16S rRNA sequence similarities with type strains of other species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that PeD5 T formed a phyletic lineage with Roseomonas stagni HS-69 T within the genus Roseomonas . On the basis of results of phenotypic, chemotaxonomic and molecular analysis, strain PeD5 T clearly represents a novel species of the genus Roseomonas , for which the name Roseomonas algicola sp. nov. is proposed. The type strain is PeD5 T (=KACC 19925 T =JCM 33309 T ).

Bacterial strain CCP-6 T , isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6 T is affiliated with species in the genus Rhodovarius . Strain CCP-6 T was most closely related to Rhodovarius lipocyclicus CCUG 44693 T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6 T were C 18 : 1 ω 7 c , C 16 : 0 and C 19 : 0 cyclo ω 8 c . The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6 T showed 85.8% average nucleotide identity and 14.5% digital DNA-DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693 T . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6 T represents a novel species in the genus Rhodovarius , for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6 T (=BCRC 81095 T =LMG 30310 T =KCTC 62188 T ).

Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll a -containing bacterial strains, KEBCLARHB70R T , KAMCLST3051 and KAMCLST3152, were isolated from the thalli of Cladonia arbuscula and Cladonia stellaris lichens. Cells from the strains were coccoid and reproduced by binary division. They were motile at the early stages of growth and utilized sugars and alcohols. All strains were psychrophilic and acidophilic, capable of growth between pH 3.5 and 7.5 (optimum, pH 5.5), and at 4-30 °C (optimum, 10-15 °C). The major fatty acids were C 18 : 1   ω7 c and C 18 : 0 ; the lipids were phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, phosphatidylglycerol, glycolipids, diphosphatidylglycerol and polar lipids with an unknown structure. The quinone was Q-10. The DNA G+C content was 67.8 mol%. Comparative 16S rRNA gene analysis together with other data, supported that the strains, KEBCLARHB70R T , KAMCLST3051 and KAMCLST3152 belonged to the same species. Whole genome analysis of the strain KEBCLARHB70R T and average amino acid identity values confirmed its distinctive phylogenetic position within the family Acetobacteraceae . Phenotypic, ecological and genomic characteristics distinguished strains KEBCLARHB70R T , KAMCLST3051 and KAMCLST3152 from all genera in the family Acetobacteraceae . Therefore, we propose a novel genus and a novel species, Lichenicoccus roseus gen. nov., sp. nov., for these novel Acetobacteraceae members. Strain KEBCLARHB70R T (=KCTC 72321 T =VKM B-3305 T ) has been designated as the type strain.

Bacterial nanocellulose (BNC) has been drawing enormous attention because of its versatile properties. Herein, we shed light on the BNC production by a novel bacterial isolate (MD1) utilizing various agro-industrial wastes. Using 16S rRNA nucleotide sequences, the isolate was identified as Komagataeibacter saccharivorans MD1. For the first time, BNC synthesis by K. saccharivorans MD1 was investigated utilizing wastes of palm date, fig, and sugarcane molasses along with glucose on the Hestrin-Schramm (HS) medium as a control. After incubation for 168 h, the highest BNC yield was perceived on the molasses medium recording 3.9 g/L with an initial concentration of (v/v) 10%. The physicochemical characteristics of the BNC sheets were inspected adopting field-emission scanning electron microscope (FESEM), atomic force microscopy (AFM), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) analysis. The FESEM characterization revealed no impact of the wastes on either fiber diameter or the branching scheme, whereas the AFM depicted a BNC film with minimal roughness was generated using date wastes. Furthermore, a high crystallinity index was estimated by XRD up to 94% for the date wastes-derived BNC, while the FTIR analyses exhibited very similar profiles for all BNC films. Additionally, mechanical characteristics and water holding capacity of the produced BNCs were studied. Our findings substantiated that expensive substrates could be exchanged by agro-industrial wastes for BNC production conserving its remarkable physical and microstructural properties.

Thermotolerant bacterial nanocellulose-producing strains, designated MSKU 9 T and MSKU 15, were isolated from persimmon and sapodilla fruits, respectively. These strains were aerobic, Gram-stain-negative, had rod-shaped cells, were non-motile and formed white-cream colonies. Phylogeny based on the 16S rRNA gene sequences revealed that MSKU 9 T and MSKU 15 represented members of the genus Komagataeibacter and formed a monophyletic branch with K. swingsii JCM 17123 T and K. europaeus DSM 6160 T . The genomic analysis revealed that overall genomic relatedness index values of MSKU 9 T with K. swingsii JCM 17123 T and K. europaeus DSM 6160 T were ~90 % average nucleotide identity (ANI) and ≤58.2 % digital DNA-DNA hybridization (dDDH), respectively. MSKU 9 T and MSKU 15 can be differentiated from the closely related K. swingsii JCM 17123 T by their growth on 30 % d-glucose and ability to utilize and to form acid from raffinose and sucrose as carbon sources, and from K. europaeus DSM 6160 T by their ability to grow without acetic acid. The genomic DNA G+C contents of MSKU 9 T and MSKU 15 were 60.4 and 60.2 mol%, respectively. The major fatty acids of MSKU 9 T and MSKU 15 were summed feature 8 (C 18 : 1   ω7c and/or C 18  : 1 ω6c). The respiratory quinone was determined to be Q10. On the basis of the results of the polyphasic taxonomic analysis, MSKU 9 T (=TBRC 9844 T =NBRC 113802 T ) represents a novel species of the genus Komagataeibacter , for which the name Komagataeibacter diospyri sp. nov. is proposed.

A heterotrophic and acidophilic bacterial strain, G45-3 T , was isolated from acidic mine drainage sampled in Fujian Province, PR China. Cells of strain G45-3 T were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Catalase and oxidase activities were positive. Strain G45-3 T grew aerobically at 20-45 °C (optimum, 37 °C) and at pH 2.5-5.0 (optimum, pH 4.0). Photosynthetic pigments were not produced. Analysis of 16S rRNA gene sequences showed that strain G45-3 T was phylogenetically related to different members of the family Acetobacteraceae , and the sequence identities to Acidisphaera rubrifaciens JCM 10600 T , Rhodovastum atsumiense G2-11 T and Rhodopila globiformis ATCC 35887 T were 95.9 , 95.3 and 95.3 %, respectively. Strain G45-3 T contained ubiquinone-10 as its respiratory quinone. The major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified aminolipid. The predominant fatty acids were cyclo-C 19 : 0 ω8 c , C 18 : 1 ω7 c , C 16 : 0 and C 18 : 0 . The genome of G45-3 T consists of one chromosome (3 907 406 bp) and three plasmids (68 344, 45 771 and 16 090 bp), with an average G+C content of 65.9 mol%. Based on the results of phenotypic and genomic analyses, it is concluded that strain G45-3 T represents a novel species of a new genus, for which the name Acidibrevibacterium fodinaquatile gen. nov., sp. nov. is proposed. A. fodinaquatile is nominated as type species and its type strain is G45-3 T (=CGMCC 1.16069 T =KCTC 62275 T ).

A Gram-stain-negative, facultatively aerobic bacterial strain, designated DB1506 T , of the family Acetobacteraceae, was isolated from an air-conditioning system in the Republic of Korea. Colonies were pink- to rosy-coloured and cells were non-motile cocci with catalase- and oxidase-positive activities. Growth of strain DB1506 T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.5 (pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl (0 %). Strain DB1506 T contained summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 1 2-OH as major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids, unidentified aminolipids and unidentified polar lipids were detected as major polar lipids. The G+C content of the genomic DNA calculated from the whole genome sequence was 72.5 mol%. Strain DB1506 T was most closely related to Paracraurococcus ruber NS89 T , Dankookia rubra WS-10 T and Siccirubricoccus deserti SYSU D8009 T with 16S rRNA gene sequence similarities of 96.01, 95.88 and 95.44 %, respectively, but strain DB1506 T formed a clearly distinct phylogenic lineage from them within the family Acetobacteraceae. On the basis of phenotypic, chemotaxonomic and molecular properties, strain DB1506 T represents a novel species of a new genus within the family Acetobacteraceae, for which the name Roseicella frigidaeris gen. nov., sp. nov. is proposed. The type strain is DB1506 T (=KACC 19791 T =JCM 32945 T ).

Bacterial nanocellulose (BNC) which is generally synthesized by several species of bacteria has a wide variety of industrial uses, particularly in the food and material industries. However, the low levels of BNC production during the fermentation process should be overcome to reduce its production cost. Therefore, in this study, we screened and identified a new cellulose-producing bacterium, optimized production of the cellulose, and investigated the morphological properties of the cellulosic materials. Out of 147 bacterial isolates from ripened fruits and traditional vinegars, strain SFCB22-18 showed the highest capacity for BNC production and was identified as Komagataeibacter sp. based on 16S rRNA sequence analysis. During 6-week fermentation of the strain using an optimized medium containing 3.0% glucose, 2.5% yeast extract, 0.24% acetic acid, 0.27% Na 2 HPO 4 , and 0.5% ethanol at 30°C, about 5 g/l of cellulosic material was produced. Both imaging and IR analysis proved that the produced cellulose would be nanoscale bacterial cellulose.

A Gram-stain-negative, strictly aerobic, catalase-positive and oxidase-positive bacterium, designated strain HR-AS T , was isolated from a water sample of the Han River located in the Republic of Korea. Cells were motile rods with a polar flagellum. Growth was observed at 5-35 °C (optimum of 25 °C) and pH 6-8 (optimum of pH 7) and in the presence of 0-2 % (w/v) NaCl (optimum of 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-AS T formed a tight phylogenic lineage with Zavarzinia compransoris LMG 5821 T . Strain HR-AS T was most closely related to Z. compransoris LMG 5821 T with a 98.7 % 16S rRNA gene sequence similarity and had very low similarities (below 91.0 %) to other type strains with validly published names. Average nucleotide identity and in silico DNA-DNA hybridization values between strain HR-AS T and Z. compransoris DSM 1231 T were 80.4 and 23.1 %, respectively. Strain HR-AS T contained ubiquinone-10 as the major quinone and homospermidine and putrescine as the major polyamines. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C16 : 0 and C18 : 1 2-OH. Strain HR-AS T contained diphosphatidylglycerol, an unidentified aminolipid and two unidentified phospholipids as major polar lipids. The DNA G+C content of strain HR-AS T was 67.2 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain HR-AS T represents a novel species of the genus Zavarzinia, for which the name Zavarziniaaquatilis sp. nov. is proposed. The type strain is HR-AS T (=KACC 19412 T =JCM 32263 T ).

Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529 T and Gluconacetobacter entanii LTH 4560 T . Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA-DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA-DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer-Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150 T [=CCM 8723 T =ZIM B1029 T ] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7 T , isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7 T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7 T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7 T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7 T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7 T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7 T (=CGMCC 1.15338 T =JCM 31140 T ).

Rhodopila globiformis: is the most acidophilic anaerobic anoxygenic phototrophic purple bacterium and was isolated from a warm acidic sulfur spring in Yellowstone Park. Its genome is larger than genomes of other phototrophic purple bacteria, containing 7248 Mb with a G + C content of 67.1% and 6749 protein coding and 53 RNA genes. The genome revealed some previously unknown properties such as the presence of two sets of structural genes pufLMC for the photosynthetic reaction center genes and two types of nitrogenases (Mo-Fe and V-Fe nitrogenase), capabilities of autotrophic carbon dioxide fixation and denitrification using nitrite. Rhodopila globiformis assimilates sulfate and utilizes the C1 carbon substrates CO and methanol and a number of organic compounds, in particular, sugars and aromatic compounds. It is among the few purple bacteria containing a large number of pyrroloquinoline quinone-dependent dehydrogenases. It has extended capacities to resist stress by heavy metals, demonstrates different resistance mechanisms to antibiotics, and employs several toxin/antitoxin systems.

Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The weaver ant Oecophylla smaragdina is an aggressive predator of other arthropods and has been employed as a biological control agent against many insect pests in plantations. Despite playing important roles in pest management, information about the microbiota of O. smaragdina is limited. In this work, a number of O. smaragdina colonies (n = 12) from Malaysia had been studied on their microbiome profile using Illumina 16S rRNA gene amplicon sequencing. We characterized the core microbiota associated with these O. smaragdina and investigated variation between colonies from different environments. Across all 12 samples, 97.8% of the sequences were assigned to eight bacterial families and most communities were dominated by families Acetobacteraceae and Lactobacillaceae. Comparison among colonies revealed predominance of Acetobacteraceae in O. smaragdina from forest areas but reduced abundance was observed in colonies from urban areas. In addition, our findings also revealed distinctive community composition in O. smaragdina showing little taxonomic overlap with previously reported ant microbiota. In summary, our work provides information regarding microbiome of O. smaragdina which is essential for establishing healthy colonies. This study also forms the basis for further study on microbiome of O. smaragdina from other regions.

Background: In recent years, the genus Asaia (Rhodospirillales: Acetobacteraceae) has been isolated from different Anopheles species and presented as a promising tool to combat malaria. This bacterium has unique features such as presence in different organs of mosquitoes (midgut, salivary glands and reproductive organs) of female and male mosquitoes and vertical and horizontal transmission. These specifications lead to the possibility of introducing Asaia as a robust candidate for malaria vector control via paratransgenesis technology. Several studies have been performed on the microbiota of Anopheles mosquitoes (Diptera: Culicidae) in Iran and the Middle East to find a suitable candidate for controlling the malaria based on paratransgenesis approaches. The present study is the first report of isolation, biochemical and molecular characterization of the genus Asaia within five different Anopheles species which originated from different zoogeographical zones in the south, east, and north of Iran., Methods: Mosquitoes originated from field-collected and laboratory-reared colonies of five Anopheles spp. Adult mosquitoes were anesthetized; their midguts were isolated by dissection, followed by grinding the midgut contents which were then cultured in enrichment broth media and later in CaCO 3 agar plates separately. Morphological, biochemical and physiological characterization were carried out after the appearance of colonies. For molecular confirmation, selected colonies were cultured, their DNAs were extracted and PCR was performed on the 16S ribosomal RNA gene using specific newly designed primers., Results: Morphological, biochemical, physiological and molecular results indicated that all isolates are members of the genus Asaia., Conclusions: Contrary to previous opinions, our findings show that Asaia bacteria are present in both insectary-reared colonies and field-collected mosquitoes and can be isolated by simple and specific methods. Furthermore, with respect to the fact that we isolated Asaia within the different Anopheles specimens from distinct climatic and zoogeographical regions, it is promising and may be concluded that species of this genus can tolerate the complicated environmental conditions of the vector-borne diseases endemic regions. Therefore, it can be considered as a promising target in paratransgenesis and vector control programs. However, we suggest that introducing the new technologies such as next generation sequencing and robust in silico approaches may pave the way to find a unique biomarker for rapid and reliable differentiation of the Asaia species.

Background: Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets)., Results: Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains., Conclusions: Variation in the gut bacterial communities of B. tryoni larvae depends on diet, domestication, and horizontal acquisition. Bacterial variation in wild larvae suggests that more than one bacterial species can perform the same functional role; however, Asaia could be an important gut bacterium in larvae and warrants further study. A greater understanding of the functions of the bacteria detected in larvae could lead to increased fly quality and performance as part of the SIT.

Bacterial cellulose (BC) is one of the prominent biopolymers that has been acquiring attention currently due to its distinctive properties and applications in various fields. The current work presents the isolation of Komagataeibacter saccharivorans strain BC1 isolated from rotten green grapes, followed by biochemical and genotypic characterization, which confirmed that the strain is capable of synthesizing cellulose. Further, production media was designed and certain variables such as carbon, nitrogen sources, pH, and temperature were optimized in order to obtain the maximum concentration of cellulose production. We found mannitol to be the ideal carbon source and yeast extract as the ideal nitrogen source with a highest BC dry yield of 1.81 ± 0.25 g/100 mL at pH 5.76 for a week at 30 °C.The charcterization of pellicles by FTIR spectrum depicted similar functional groups present in synthesized BC as that of the commercial cellulose. X-ray diffraction revealed that BC showed 82% crystallinity. Surface morphology of the dried pellicle was studied by SEM image which showed that the BC surface was tightly packed with thin fibers with less porosity. Hence the study demonstrates that the isolates of K.saccharivorans could be used to produce a biopolymer in a short period of time using a modified production medium.

A Gram-stain-negative, ovoid-shaped, aerobic, non-motile, catalase- and oxidase-positive, and moderately thermophilic bacterial strain, designated strain YIM 72346 T , was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth occurred at 37-50 °C (optimum, 45 °C), at pH 6.0-9.0 (optimum, pH 6.5-7.0) and in the presence of 0.5-1.0 % (w/v) NaCl (optimum, 0.5 %). The major cellular fatty acids were C18 : 1ω7c, C16 : 0, C19 : 0cyclo ω8c,and C18 : 1 2-OH. The genomic DNA G+C content was determined to be 69.8 mol%. The predominant ubiquinone was Q-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified phospholipids. Bacteriochlorophyll α and carotenoic acids were not detected. Strain YIM 72346 T was not observed for the accumulation of poly-β-hydroxybutyrate. The strain shared highest 16S rRNA gene sequence identities with Crenalkalicoccus roseus YIM 78023 T (93.3 %) and Craurococcus roseus NS130 T (92.7 %), but formed a distinct lineage within the family Acetobacteraceae in the phylogenetic trees. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 72346 T is considered to represent a novel genus and species of the family Acetobacteraceae, for which the name Caldovatus sediminis gen. nov., sp. nov. is proposed. The type strain of Caldovatus sediminis is YIM 72346 T (=KCTC 52714 T =CGMCC 1.16330 T ).

A novel acidophilic heterotrophic bacterium, strain Ok2G T , was isolated from a freshwater lake in Japan. Cells of the isolate were Gram-stain-negative and non-motile rods (0.6-0.8×1.0-2.8 µm). Growth was observed at 4-35 °C with an optimum growth temperature of 28 °C. The pH range for growth was 3.0-6.2 with an optimum pH of 4.5. The strain utilized fructose, glucose, sucrose, mannitol, sorbitol, ethanol, benzyl alcohol, pyruvate, yeast extract and tryptone as carbon and energy sources for aerobic growth. DNA G+C content was 62.6 mol%. The major cellular fatty acid and the isoprenoid quinone were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and Q-10, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain Ok2G T belongs to the genus Acidocella but is distinct from existing species with sequence similarities lower than 97 %. On the basis of these results, strain Ok2G T (=NBRC 112502 T =DSM 104037 T ) is proposed as the type strain of a novel species, Acidocellaaquatica sp. nov.

Strain SYSU D8009 T was isolated from a desert sample collected from Saudi Arabia. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, non-motile, aerobic and non-spore-forming. It was able to grow at 4-45 °C and pH 4.0-8.0, and exhibited NaCl tolerance of up to 1.5 % (w/v). Strain SYSU D8009 T shared the closest 16S rRNA gene sequence similarities with members of the family Acetobacteraceae, with a value of less than 96.0 %. In the phylogenetic dendrograms, the strain clustered with the genera Paracraurococcus, Craurococcus and Crenalkalicoccus within the family Acetobacteraceae but with a distinct lineage, thereby demonstrating that the strain should be classified within the family Acetobacteraceae. The respiratory ubiquinone was found to be Q-10. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminolipids. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The genomic DNA G+C content of strain SYSU D8009 T was determined to be 71.6 mol%. Based on the results of the phylogenetic analyses and differences in the physiological and biochemical characteristics, strain SYSU D8009 T merits representation of a novel species of a new genus within the family Acetobacteraceae, for which the name Siccirubricoccus deserti gen. nov., sp. nov. is proposed. The type strain of Siccirubricoccus deserti sp. nov. is SYSU D8009 T (=CGMCC 1.15936 T =KCTC 62088 T ).

As part of a study to investigate the microbial diversity in the intestine of Apis mellifera, we isolated strain MRM1T from the midgut. MRM1T was a Gram-stain-negative, strictly aerobic, non-motile, non-spore forming and rod-shaped bacteria. Creamy beige-coloured colonies were circular with entire margins in Lactobacilli MRS agar. The strain grew at 25-37 °C (optimum, 30-37 °C) and at a pH range of 4.0 to 9.0 (optimum pH, 7.0-8.5). The strain tolerated 0-1 % (w/v) NaCl (optimal growth occurred in the absence of NaCl). On the basis of the results of a phylogenetic analysis based on the 16S rRNA gene sequences, we determined that MRM1T represents a member of the genus Bombella with the highest sequence similarity to Bombella intestini LMG 28161T (98.8 %). The major quinone was Q10, and dominant fatty acids (>10 %) were C19 : 0cyclo ω8c (33.6 %), C16 : 0 (22.2 %), C18 : 1ω7c (15.9 %) and C14 : 0 (12.5 %). The polar lipid profile of MRM1T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified phospholipid and four unidentified lipids. The DNA G+C content of MRM1T was 59.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, MRM1T represents a novel species of the genus Bombella, for which the name Bombella apis sp. nov. is proposed with the type strain MRM1T (=KCTC 52452T=JCM 31623T).

Objective: The genus Roseomonas comprises a group of pink-pigmented, slow-growing, aerobic, non-fermentative Gram-negative bacteria, which have been isolated from environmental sources such as water and soil, but are also associated with human infections. In the study presented here, Roseomonas mucosa was identified for the first time as part of the endodontic microbiota of an infected root canal and characterised in respect to growth, antibiotic susceptibility and biofilm formation., Results: The isolated R. mucosa strain showed strong slime formation and was resistant to most β-lactam antibiotics, while it was susceptible to aminoglycosides, carbapenemes, fluorochinolones, polymyxines, sulfonamides and tetracyclines. Biofilm formation on artificial surfaces (glass, polystyrene, gutta-percha) and on teeth was tested using colorimetric and fluorescence microscopic assays. While solid biofilms were formed on glass surfaces, on the hydrophobic surface of gutta-percha points, no confluent but localised, spotty biofilms were observed. Furthermore, R. mucosa was able form biofilms on dentin. The data obtained indicate that R. mucosa can support establishment of endodontic biofilms and furthermore, infected root canals might serve as an entrance pathway for blood stream infections by this emerging pathogen.

A bacterial cellulose (BC) producing strain isolated from fermented fruit juice was identified as Komagataeibacter intermedius (K. intermedius) FST213-1 by 16s rDNA sequencing analysis and biochemical characteristics test. K. intermedius FST213-1 can produce BC within pH 4-9 and exhibit maximum BC production (1.2g/L) at pH 8 in short-term (4-day) cultivation. Results of Fourier transform infrared spectroscopy, X-ray diffraction, water content, thermogravimetric analysis and mechanical property indicated that BC produced from K. intermedius FST213-1 exhibits higher water content ability (99.5%), lower thermostability (315°C), lower crystallinity (79.3%) and similar mechanical properties in comparison with the specimen from model BC producer, Gluconacetobacter xylinus 23769. Based on these analyses, the novel based-resistant strain K. intermedius FST213-1 can efficiently produce BC, which can be applied for industrial manufacturing with potential features., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Pines in the subalpine environment at Niwot Ridge, CO, have been found to host communities of acetic acid bacteria (AAB) within their needles. The significance and ubiquity of this pattern is not known, but recent evidence of nitrogen (N)-fixing activity in Pinus flexilis (limber pine) foliage calls for a better understanding of the processes that regulate endophytic communities in forest tree canopies. Here, to test if AAB dominate the foliar bacterial microbiota in other subalpine locations, we compared the 16S rRNA community in needles from P. flexilis and P. contorta (lodgepole pine) growing in the Eastern Sierra Nevada, CA, and Niwot Ridge, CO. AAB made up the majority of the bacterial community in both species at both sites. Multiple distinct AAB taxa, resolved at the single nucleotide level, were shared across host species and sites, with dominant OTUs identical or highly similar to database sequences from cold environments, including high altitude air sampled in Colorado, and the endosphere of Arctic plants. Our results suggest strong selection for community composition, potentially amplified by the long lifespan of individual Pinus needles, along with low dispersal constraints on canopy bacteria., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Symbiotic associations between gut microbiota and their animal hosts shape the evolutionary trajectories of both partners. The genomic consequences of these relationships are significantly influenced by a variety of factors, including niche localization, interaction potential, and symbiont transmission mode. In eusocial insect hosts, socially transmitted gut microbiota may represent an intermediate point between free living or environmentally acquired bacteria and those with strict host association and maternal transmission., Results: We characterized the bacterial communities associated with an abundant ant species, Camponotus chromaiodes. While many bacteria had sporadic distributions, some taxa were abundant and persistent within and across ant colonies. Specially, two Acetobacteraceae operational taxonomic units (OTUs; referred to as AAB1 and AAB2) were abundant and widespread across host samples. Dissection experiments confirmed that AAB1 and AAB2 occur in C. chromaiodes gut tracts. We explored the distribution and evolution of these Acetobacteraceae OTUs in more depth. We found that Camponotus hosts representing different species and geographical regions possess close relatives of the Acetobacteraceae OTUs detected in C. chromaiodes. Phylogenetic analysis revealed that AAB1 and AAB2 join other ant associates in a monophyletic clade. This clade consists of Acetobacteraceae from three ant tribes, including a third, basal lineage associated with Attine ants. This ant-specific AAB clade exhibits a significant acceleration of substitution rates at the 16S rDNA gene and elevated AT content. Substitutions along 16S rRNA in AAB1 and AAB2 result in ~10 % reduction in the predicted rRNA stability., Conclusions: Combined, these patterns in Camponotus-associated Acetobacteraceae resemble those found in cospeciating gut associates that are both socially and maternally transmitted. These associates may represent an intermediate point along an evolutionary trajectory manifest most extremely in symbionts with strict maternal transmission. Collectively, these results suggest that Acetobacteraceae may be a frequent and persistent gut associate in Camponotus species and perhaps other ant groups, and that its evolution is strongly impacted by this host association.

Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats.

The genus Asaia has gained much interest lately owing to constant new species discoveries and its role as a potential opportunistic pathogen to humans. Here we describe a transient bacteremia due to Asaia lannensis in a patient with a psychiatric disorder (compulsive self-injection of different substances). Common phenotypic methods of identification failed to identify this organism, and only restriction fragment lenght polymorphism of PCR-amplified 16S rRNA gene allowed for proper identification. The isolate was highly resistant to most antibiotics. The paper also discusses the currently available medical literature, acknowledges the potential problems linked to the isolation of these strains and proposes an approach to species identification that can be applied in a clinical microbiology laboratory.

The acetic acid bacteria have mainly relevance for bacterial cellulose production and fermented bio-products manufacture. The purpose of this study was to identify temperate bacteriophages in a cellulose-producing bacterial strain Komagataeibacter intermedius IMBG180. Prophages from K. intermedius IMBG180 were induced with mitomycin C and nalidixic acid. Transmission electron microscopy analysis exhibited tailed bacteriophages belonging to Myoviridae. A PCR assay targeting the capsid gene of the myoviruses proved phylogenetic position of induced phages. Nalidixic acid was poor inducer of prophages, however, it induced the OMV-like particles release. Size of OMVs depended on an antibiotic applied for phage induction and varied in the range of 30-80 and 120-200 nm. Inside some of them, tails of phages have been visible. Under conditions, inducing prophages, OMVs acted as the collectors of formed phage particles, using outer membrane receptors for phage detection (in this case, outer membrane siderophore receptor), and fulfilled therefore "a cleaning," as well as defensive functions, preventing bacteriophage spread outside population. This is the first description of myoviruses affiliated to K. intermedius, as well as outer membrane vesicles interaction with phages within this host., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species., (© 2015 IUMS.)

The honey bee hive environment contains a rich microbial community that differs according to niche. Acetobacteraceae Alpha 2.2 (Alpha 2.2) bacteria are present in the food stores, the forager crop, and larvae but at negligible levels in the nurse and forager midgut and hindgut. We first sought to determine the source of Alpha 2.2 in young larvae by assaying the diversity of microbes in nurse crops, hypopharyngeal glands (HGs), and royal jelly (RJ). Amplicon-based pyrosequencing showed that Alpha 2.2 bacteria occupy each of these environments along with a variety of other bacteria, including Lactobacillus kunkeei. RJ and the crop contained fewer bacteria than the HGs, suggesting that these tissues are rather selective environments. Phylogenetic analyses showed that honey bee-derived Alpha 2.2 bacteria are specific to bees that "nurse" the hive's developing brood with HG secretions and are distinct from the Saccharibacter-type bacteria found in bees that provision their young differently, such as with a pollen ball coated in crop-derived contents. Acetobacteraceae can form symbiotic relationships with insects, so we next tested whether Alpha 2.2 increased larval fitness. We cultured 44 Alpha 2.2 strains from young larvae that grouped into nine distinct clades. Three isolates from these nine clades flourished in royal jelly, and one isolate increased larval survival in vitro. We conclude that Alpha 2.2 bacteria are not gut bacteria but are prolific in the crop-HG-RJ-larva niche, passed to the developing brood through nurse worker feeding behavior. We propose the name Parasaccharibacter apium for this bacterial symbiont of bees in the genus Apis., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

Investigations of microbiota within mosquitoes continue to widen the spectrum of possible symbiont-based applications against vector-borne diseases. In this context, α-proteobacteria of the genus Asaia (Rhodospirillales: Acetobacteraceae) are emerging as possible endosymbiotic candidates, particularly in paratransgenic approaches aimed at interrupting pathogen transmission. Previous studies have shown that Asaia spp. distribution among Anopheles gambiae and Anopheles stephensi (Diptera: Culicidae) mosquitoes displayed positive rates of infection in isolated midguts, salivary glands and reproductive tissues. Similarly, Asaia has been detected in Aedes albopictus (Stegomyia albopicta) and Aedes aegypti (Stegomyia aegypti) (Diptera: Culicidae) populations. Within the Culex pipiens complex (Diptera: Culicidae), Asaia infection is still largely unexplored. Here, we summarize a preliminary survey of laboratory-reared Cx. pipiens complex and field-collected Culex quinquefasciatus for the presence of Asaia spp., and present the first identification of Asaia in some of the members of the Cx. pipiens complex and the first description in West African populations of Cx. quinquefasciatus., (© 2013 The Royal Entomological Society.)

Several thermo- and mesoacidophilic bacterial strains that revealed high lipolytic activity were isolated from water samples derived from acidic hot springs in Los Nevados National Natural Park (Colombia). A novel lipolytic enzyme named 499EST was obtained from the thermoacidophilic alpha-Proteobacterium Acidicaldus USBA-GBX-499. The gene estA encoded a 313-amino-acid protein named 499EST. The deduced amino acid sequence showed the highest identity (58 %) with a putative α/β hydrolase from Acidiphilium sp. (ZP&#95;08632277.1). Sequence alignments and phylogenetic analysis indicated that 499EST is a new member of the bacterial esterase/lipase family IV. The esterase reveals its optimum catalytic activity at 55 °C and pH 9.0. Kinetic studies showed that 499EST preferentially hydrolyzed middle-length acyl chains (C6-C8), especially p-nitrophenyl (p-NP) caproate (C6). Its thermostability and activity were strongly enhanced by adding 6 mM FeCl3. High stability in the presence of water-miscible solvents such as dimethyl sulfoxide and glycerol was observed. This enzyme also exhibits stability under harsh environmental conditions and enantioselectivity towards naproxen and ibuprofen esters, yielding the medically relevant (S)-enantiomers. In conclusion, according to our knowledge, 499EST is the first thermoalkalostable esterase derived from a Gram-negative thermoacidophilic bacterium.

Unlabelled: Animal-associated bacteria (microbiota) affect host behaviors and physiological traits. To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. First, we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains. The effects of monoassociation on host traits were not confined to particular taxonomic groups. Second, we clustered protein-coding sequences of the bacteria by sequence similarity de novo and statistically associated the magnitude of the host trait with the bacterial gene contents. The animals had been monoassociated with genome-sequenced bacteria, so the metagenome content was unambiguous. This analysis showed significant effects of pyrroloquinoline quinone biosynthesis genes on development time, confirming the results of a published transposon mutagenesis screen, thereby validating the MGWA; it also identified multiple genes predicted to affect host TAG content, including extracellular glucose oxidation pathway components. To test the validity of the statistical associations, we expressed candidate genes in a strain that lacks them. Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls. Consistent with the prediction that glucose oxidation pathway gene expression increased bacterial glucose utilization, the glucose content of the host diet was reduced when flies were exposed to these strains. Our findings indicate that microbiota affect host nutritional status through modulation of nutrient acquisition. Together, these findings demonstrate the utility of MGWA for identifying bacterial determinants of host traits and provide mechanistic insight into how gut microbiota modulate the nutritional status of a model host., Importance: To understand how certain gut bacteria promote the health of their animal hosts, we need to identify the bacterial genes that drive these beneficial relationships. This task is challenging because the bacterial communities can vary widely among different host individuals. To overcome this difficulty, we quantified how well each of 41 bacterial species protected Drosophila fruit flies from high fat content. The genomes of the chosen bacterial strains were previously sequenced, so we could statistically associate specific bacterial genes with bacterially mediated reduction in host fat content. Bacterial genes that promote glucose utilization were strongly represented in the association, and introducing these genes into the gut bacteria was sufficient to lower the animal's fat content. Our method is applicable to the study of many other host-microbe interactions as a way to uncover microbial genes important for host health., (Copyright © 2014 Chaston et al.)

The objective of this study was to investigate the adhesion of isolated spoilage bacteria to packaging materials used in the food industry. Microorganisms were isolated from commercial fruit-flavored mineral water in plastic bottles with flocks as a visual defect. The Gram-negative rods were identified using the molecular method through the amplification of a partial region of the 16S rRNA gene. Based on the sequence identity (99.6%) between the spoilage organism and a reference strain deposited in GenBank, the spoilage isolate was identified as Asaia bgorensis. Experiments on bacterial adhesion were conducted using plates made of glass and polystyrene (packaging materials commonly used in the beverage industry). Cell adhesion ability was determined using luminometry, plate count, and the microscopic method. The strain of A. bogorensis was characterized by strong adhesion properties which were dependent on the surface type, with the highest cell adhesion detected on polystyrene.

A Gram-negative, aerobic, non-motile, non-spore-forming, cocci-shaped, red-pigmented bacterium, designated strain PB-K8(T), was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed that the isolate was clearly affiliated with the class Alphaproteobacteria, and was most closely related to Belnapia moabensis DSM 16746(T) and Belnapia rosea DSM 23312(T), showing a 16S rRNA gene sequence similarity to the type strains of each species of 98.4 and 97.2%, respectively. The cells of strain PB-K8(T) formed red colonies on R2A agar, contained Q-9 as the predominant ubiquinone and included summed feature 3 (C16:1ω7c C16:1ω6c), C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C18:1 2-OH and C19:0 cyclo ω8c as the major fatty acids. The G+C content of the genomic DNA of strain PB-K8(T) was 72.1 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB-K8(T) represents a novel species of the genus Belnapia, for which the name Belnapia soli sp. nov. is proposed. The type strain is PB-K8(T) (=KCTC 23765(T)=JCM 18033(T)).

A bacterial strain designated M1MS02(T) was isolated from a surface-sterilized nodule of Medicago sativa in Zamora (Spain). The 16S rRNA gene sequence of this strain showed 96.5 and 96.2 % similarity, respectively, with respect to Gluconacetobacter liquefaciens IFO 12388(T) and Granulibacter bethesdensis CGDNIH1(T) from the family Acetobacteraceae. The novel isolate was a Gram-stain-negative, non-sporulating, aerobic coccoid to rod-shaped bacterium that was motile by a subpolar flagellum. The major fatty acid was C18 : 1ω7c and the major ubiquinone was Q-10. The lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, three aminolipids, four glycolipids, two phospholipids and one lipid. Strain M1MS02(T) was catalase-positive and oxidase- and urease-negative. Acetate and lactate were not oxidized. Acetic acid was produced from ethanol in culture media supplemented with 2 % CaCO3. Ammonium sulphate was assimilated in glucose medium. The strain produced dihydroxyacetone from glycerol. Phylogenetic and phenotypic analyses commonly used to differentiate genera within the family Acetobacteraceae showed that strain M1MS02(T) should be classified as representing a novel species of a new genus within this family, for which the name Endobacter medicaginis gen. nov., sp. nov. is proposed. The type strain of the type species is M1MS02(T) ( = LMG 26838(T) = CECT 8088(T)). To our knowledge, this is the first report of a member of the Acetobacteraceae occurring as a legume nodule endophyte.

A Gram-staining-negative, pale-pink-pigmented, non-motile, obligately aerobic and rod-shaped bacterium, designated strain W37(T), was isolated from soil and subjected to a taxonomic investigation using a polyphasic approach. The strain grew at 1-30 °C, oxidized thiosulfate and accumulated polyhydroxyalkanoates. Photosynthetic pigments were represented by bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W37(T) was most closely related to members of the genera Roseococcus and Rubritepida (with sequence similarities of <92.8 %) but formed a distinct lineage in the family Acetobacteraceae. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified aminolipids and one other unidentified lipid. The predominant cellular fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain W37(T) was 68.2 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain W37(T) represents a novel species of a new genus in the family Acetobacteraceae, for which the name Humitalea rosea gen. nov., sp. nov. is proposed. The type strain of the type species is W37(T) ( = CIP 110261(T) = LMG 26243(T)).