16S rDNA Sequence Analysis Research Articles

Characterization and host range assessment of Dickeya zeae associated with pineapple soft rot disease in East Lampung, Indonesia

Abstract. Aeny TN, Suharjo R, Ginting C, Hapsoro D, Niswati A. 2020. Characterization and host range assessment of Dickey zeae associated with pineapple soft rot disease in East Lampung, Indonesia. Biodiversitas 21: 587-595. The study aims to characterize the Dickeya zeae associated with pineapple soft rot in East Lampung, Indonesia and to assess the bacterial host range. From the blister-like lesion-symptom, bacteria were isolated with the morphological characteristics: circular, convex, cream white milk-colored, with diameter colonies ranging from 1-2 mm in diameter. Two strains (N-Unila 5 and N-Unila 10) were selected for further investigation including pathogenicity test on pineapple seedling, species identification by phenotypic characteristics and molecular techniques using sequence analysis of 16SrDNA, recA, and dnaX as well as host range test on 25 different plant species. The result of the pathogenicity test showed similar symptoms to those observed in the field. Physiological and biochemical characterization revealed that the two isolates were Gram-negative bacteria, fermentative, lecithinase positive, non-fluorescent on King’s B medium, able to grow on YDC medium at 41oC, did not produce H2S and did not grow in the presence of 5% NaCl. The isolates capable of using Myo-inositol, M-tartrate, mannitol, L-tartrate, lactose, glycerol, D-melibiose, D-arabinose, citrate, and cis-aconitic acid but did not utilize starch, S-ketoglucanate, L-ascorbic acid, inulin, folic acid, D-raffinose and tartrate as a sole carbon source. Phenotypic characteristics indicated that the strains were in the group of Dickeya spp. bv. 3 (phenon 1). Sequence analysis of 16S rDNA, recA, and dnaX revealed that the strains were placed in the same cluster with the reference strain of D. zeae. Host range assessment showed positive soft rot symptoms in Aloe vera, chinese cabbage, dragon-fruit, eggplant, lettuce, and welsh onion that have never been reported before.

Molecular identification of two Sarcocystis species in fallow deer (Dama dama) from Lithuania

Due to the lack of molecular research conducted, little is known about Sarcocystis species diversity in the fallow deer (Dama dama). Until now, Sarcocystis jorrini and Sarcocystis morae were described to form sarcocysts in the muscles of this host. In the present study diaphragm muscle samples of free-ranging fallow deer from Lithuania were investigated for Sarcocystis species. Sarcocysts were detected in 39 out of 48 (81.3%) fallow deer examined. Under a light microscope two types of sarcocysts having hair-like and finger-like protrusions were observed. Based on DNA sequence analysis of cox1 and 18S rDNA, two species, S. morae and Sarcocystis entzerothi were identified. In prior studies, the latter species was only detected in Lithuanian roe deer (Capreolus capreolus) and in sika deer (Cervus nippon). The haplotype network of S. morae sequences specified close relationships between haplotypes found in the same country. According to current knowledge, the fallow deer is characterised by low Sarcocystis species richness as compared with other cervid species from Europe.

Levan from a new isolated Bacillus subtilis AF17: Purification, structural analysis and antioxidant activities

A strain of Bacillus subtilis AF 17 with high exopolysaccharide (EPS) production ability was isolated and identified based on morphological and physiological characteristics and phylogenetic analysis of 16S rDNA sequences. EPS was isolated from the strain fermentation broth by alcohol precipitation and gel-filtration chromatography. Its structural characteristics were investigated and elucidated by methylation analysis, gas chromatography mass spectrometry and nuclear magnetic resonance spectroscopy. Based on the obtained data, the EPS was found to be a levan containing a backbone of 6-substituted β-fructoses, with a low grade of branching at position 1 (linear/branched ratio 20:1). Levan showed a molecular weight of about 20 MDa. The antioxidant activity of this biopolymer was studied and revealed that levan showed an interesting 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging capacity (IC50 levan = 1.42 mg/mL), reducing power, and also a strong total antioxidant activity. Overall, the results suggest that levan is a promising source of natural antioxidants and can be used as additive in food and pharmaceutical preparations.

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

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593T (97.7% similarity) and Paenibacillus macerans ATCC 8244T (97.6% similarity). Draft genome of strain ChDC PVNT-B20T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3mol%. Average nucleotide identity values between strain ChDC PVNT-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20T were anteiso-C15:0 (43.4%), C16:0 (16.6%), iso-C16:0 (14.4%), and anteiso-C17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20T (= KCOM 3021T = JCM 33462T).

Improved degradation of n-hexane vapours using a hybrid system, a photoreactor packed with TiO2 coated-scoria granules and a multilayer biofilter.

Biofiltration of hydrophobic and/or recalcitrant volatile organic compounds such as n-hexane is imperfect. In the present study, we applied a hybrid system consisting of a photoreactor packed with scoria granules coated with TiO2 and a biofilter to improve the removal efficiency of n-hexane from the air stream. The experimental results showed that the hybrid system provided higher removal efficiencies than the single biofilter process with an inlet n-hexane concentration range of 0.11-1g-3 for empty bed residence times (EBRTs) of 30-120s in the hybrid system. The removal efficiency of the single biofilter in EBRTs of 30, 60 and 120s was 10.06%, 21.45%, and 45.98%, respectively. When the photoreactor was included as a pretreatment system (with residence time of 7-27s) and the overall EBRTs of the system was adjusted to 30, 60 and 120s, the removal efficiency of the hybrid system was increased to 39.79%, 63.08%, and 92.6%, respectively. The mass ratio of carbon dioxide produced as an indicator for n-hexane degradation in the hybrid system and the biofilter alone was 1.9 and 1.28, respectively. Bacterial community analysis with sequence analysis of 16S rDNA in the biofilter biomass revealed that Pseudomonas and Bacillus as predominant bacterial species were responsible for n-hexane biodegradation. Therefore, the application of the hybrid system is advantageous in enhanced n-hexane removal from the air stream.

Molecular study of a phytoplasma associated with safflower fasciation in Iran

A safflower disease was observed in the fields of South Khorasan (Iran) in 2017–2018. Affected plants had extensive fasciation, bushy growth, small leaves, phyllody and shortened internodes. Polymerase chain reaction (PCR) assays were performed using universal phytoplasma primers pairs P1/P7, R16mF1/mR1 and M1/M2 to detect putative phytoplasma (s). Nested PCR analyses showed that all symptomatic plants were positive for phytoplasma infection, while asymptomatic plants were negative. Nucleotide sequence analysis and RFLP analyses of PCR-amplified 16S rDNA sequences indicated that safflower fasciation in Iran was associated with a phytoplasma that belonged to the peanut witches' broom group (16SrII). Phylogenetic analysis confirmed that safflowers fasciation phytoplasma (SaP) must be classified in ‘Candidatus phytoplasma aurantifolia’ (16SrII) taxonomic group. To our knowledge, this is the first documentation of a phytoplasma associated with safflower fasciation in Iran and the world.

Characterisation of Pb-resistant plant growth-promoting rhizobacteria (PGPR) from Scirpus grossus

Abstract Microorganisms that have the potential to improve plant productivity and health are known as plant growth-promoting rhizobacteria. Rhizobacteria play a major role in phytoremediation process by increasing the phytoremediation efficiency, thus the need to identify the superior rhizosphere bacteria has been gaining serious attention. In the current study, Scirpus grossus were exposed to a series of lead-contaminated sand (50, 100, 150, 200 and 300 mg/L) in plastic crates in greenhouse enviroment. Four weeks after exposure, the plants could sustain with toxicity of lead contamination by as much as 300 mg/L. Twenty two colonies of rhizobacteria were isolated from plant roots of Scirpus grossus. The rhizobacteria were characterised based on cell and colony observation. Identification of rhizobacteria was carried out based on analysis of 16S rDNA sequences and were identified as Aeromonas taiwanensis isolate 5E, Bacillus sp. Isolate 7G, Bacillus cereus isolate 8H and 3C , Bacillus velezensis isolate 9I, Bacillus proteolyticus isolate 4D, Bacillus stratosphericus isolate 14N, Bacillus megaterium isolate 11K , Pseudomonas sp. Isolate 12L , Enterobacter cloacae isolate 13M and isolate 16P, Bacillus aerius isolate 15O and Lysinibacillus sp. isolate 10J. The highly lead-resistant rhizobacteria were identified as Bacillus proteolyticus isolate 4D, Bacillus velezensis isolate 9I and Lysinibacillus sp. isolate 10J , which can tolerate against high concentration of lead (300 mg/L). The results showed that these highly lead-resistant rhizobacteria have potential to produce plant growth-promoting traits and have a ability to help S. grossus growth and productivity.

Isolation and identification of an isoflavone reducing bacterium from feces from a pregnant horse.

The aim of this research was to isolate bacteria capable of biotransforming daidzein from fresh feces from pregnant horses. A Hungate anaerobic roller tube was used for anaerobic culture. Single colonies were picked at random and incubated with daidzein. High performance liquid chromatography was used to detect whether the isolated bacteria were able to biotransform the substrate. A strain capable of reducing daidzein was selected and characterized using sequence analysis of 16S rDNA, and a phylogenetic tree was constructed. The morphological physiological and biochemical characteristics of the strain were investigated. A facultative anaerobic, Gram-positive bacterium capable of converting daidzein to dihydrodaidzein was isolated and named HXBM408 (MF992210). A BLAST search of HXBM408's 16S rDNA sequence against the GenBank database suggested that the strain has 99% similarity with Pediococcus acidilactici strain DSM (NR042057). The morphological, physiological, and biochemical characteristics of HXBM408 are very similar to those of Pediococcus. Based on these characteristics, the strain was identified as Pediococcus acidilactici. The bacterial strain HXBM408 isolated from the feces of pregnant horses was able to reduce the isoflavone daidzein to dihydrodaidzein.

Description of Echthrogaleus spinulus n. sp. (Copepoda: Pandaridae) parasitic on a torpedo ray from the central Pacific Ocean utilising a morphological and molecular approach.

A new species of parasitic copepod, Echthrogaleus spinulus n. sp. (Pandaridae), is described from the torpedo ray Tetronarce tokionis (Tanaka) (Torpedinidae) captured in pelagic Hawaiian waters. The new species has pediger 4 bearing large dorsal plates with denticles on posterior margin, genital complex with posterolateral lobes widely curved medially and overlapping, leg 4 exopod incompletely 3-segmented, and the largest body size (maximum length 16 mm from anterior rim of frontal plates to tip of caudal rami, excluding setae). This morphology does not match any of the seven valid species of Echthrogaleus Steenstrup & Lütken, 1861. Analysis of 28S rDNA sequences separated the new material from the Central Pacific from samples of E. coleoptratus in the Atlantic and Eastern Pacific Oceans. However, due to the lack of DNA sequences in the databases, the new 28S rDNA sequence cannot used to confirm the species identity. The unique morphological characteristics of the Central Pacific female copepods combined with 28S rDNA sequencing was used as a basis to validate the new species.

Administration of Akkermansia muciniphila Ameliorates Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice.

Inflammatory bowel diseases (IBDs) develop as a result of complex interactions among genes, innate immunity and environmental factors, which are related to the gut microbiota. Multiple clinical and animal data have shown that Akkermansia muciniphila is associated with a healthy mucosa. However, its precise role in colitis is currently unknown. Our study aimed to determine its protective effects and underlying mechanisms in a dextran sulfate sodium (DSS)-induced colitis mouse model. Twenty-four C57BL/6 male mice were administered A. muciniphila MucT or phosphate-buffered saline (PBS) once daily by oral gavage for 14 days. Colitis was induced by drinking 2% DSS from days 0 to 6, followed by 2 days of drinking normal water. Mice were weighed daily and then sacrificed on day 8. We found that A. muciniphila improved DSS-induced colitis, which was evidenced by reduced weight loss, colon length shortening and histopathology scores and enhanced barrier function. Serum and tissue levels of inflammatory cytokines and chemokines (TNF-α, IL1α, IL6, IL12A, MIP-1A, G-CSF, and KC) decreased as a result of A. muciniphila administration. Analysis of 16S rDNA sequences showed that A. muciniphila induced significant gut microbiota alterations. Furthermore, correlation analysis indicated that pro-inflammatory cytokines and other injury factors were negatively associated with Verrucomicrobia, Akkermansia, Ruminococcaceae, and Rikenellaceae, which were prominently abundant in A. muciniphila-treated mice. We confirmed that A. muciniphila treatment could ameliorate mucosal inflammation either via microbe-host interactions, which protect the gut barrier function and reduce the levels of inflammatory cytokines, or by improving the microbial community. Our findings suggest that A. muciniphila may be a potential probiotic agent for ameliorating colitis.

Distribution and genetic diversity of the parasitic dinoflagellate Amoebophrya in coastal waters of China

Amoebophrya is an obligate endoparasite infecting wide ranges of marine organisms in coastal and oceanic waters. The parasitoid has received growing attention, due to its enormous genetic diversity in seawaters and suppressive effects on the growth of host dinoflagellates. Harmful algal blooms (HABs) caused by planktonic dinoflagellates have significantly impacted the coastal environment and mariculture in China. Series of studies have been conducted to reveal the occurrence mechanism and negative impacts of HABs in past decades, while the factors contributing to the recession of HABs have rarely been studied. Thus, the host range, prevalence and diversity of Amoebophrya along the coastline of China were systemically investigated to facilitate future studies on the ecological roles of the parasitoid. Overall, 10 dinoflagellate taxa were found to be infected by Amoebophrya spp., and the prevalence ranged from 0.03% to 2.50%. Sequencing of environmental genomic DNA revealed substantial diversity and significant regional heterogeneity of Amoebophryidae sequences derived from 12 coastal bays, while no significant correlation was observed among geographical locations. Phylogenetic analyses of 18S rDNA sequences derived from individual Amoebophrya-infected cells indicated the host divergence of the parasitoid and lend credence to the multiple species assumption. The results further revealed the broad host range, wide distribution and substantial diversity of Amoebophrya in the coastal waters of China, that should not be neglected in future studies on the succession of HABs, as well as the ecological significance of this parasitoid in marine microbial food webs.

Biocontrol and plant growth-promoting ability of plant-associated bacteria from tomato (Lycopersicum esculentum) under field condition

Forty-five bacterial isolates recovered from surface-sterilized root, stem and leaf tissues of tomato were studied for their antifungal activity against phytopathogens, and plant growth-promoting (PGP) and biocontrol traits. Six plant-associated bacteria suppressed all the pathogens tested under in vitro plate assay and also shown PGP and biocontrol traits. The six isolates showing PGP and biocontrol properties were identified as Bacillus spp., based on the microbial identification system (Biolog) and partial sequence analysis of 16S rDNA. Two independent field trials were conducted with biocontrol bacteria along with chemical control (Thiram+Fytolan) and control (Without treatment). The averaged results of two field trails revealed that tomato plants inoculated with BETS11 (11.73 t/ha) and BETR11 (11.24 t/ha) strains showed significantly higher yield and disease reduction on par with chemical control (11.81 t/ha). However, there was an increase in the yield with respect to uninoculated control except the isolate BETS5 (9.09 t/ha). Therefore, the isolates BETS11 and BETR11 may be used as efficient biofertilizer and bio-control agent for tomato production in the Island agricultural ecosystem.

Report of a mermithid nematode infecting Amyna axis, Chrysodeixis spp. and Spodopteraspp.from India

Amyna axis (Lepidoptera: Erebidae), Chrysodeixis spp. ( C. acuta and C. eriosoma ) and Spodoptera spp. ( S. exigua and S. litura ) (Lepidoptera: Noctuidae) are important polyphagous insect-pests of leguminous crops. A mermithid (Nematoda: Mermithidae) nematode was found parasitizing the larval stages of these insects in the western Indian state of Rajasthan. Morphological and molecular analysis suggests that the nematode might be a species of the genus Hexamermis . The average length of post-parasitic nematode juveniles was 15 cm, and the average greatest body width was 1.5 mm. The vulva was median (V% = 48) without vulval flap. Approximately 100-125 μm long caudal appendages were present on tail. The cross-section revealed the presence of six hypodermal chords at the mid body region, and stichosome was present. The 18S rDNA sequence showed 99% similarity to mermithid nematode. A phylogenetic analysis of 18S rDNA sequences of mermithids resulted in identification of a new clade “Lineage 3” which included representatives of Mermis sp., Isomermis sp., Limnomermis sp., and Pheromermis sp. This is the first report of natural mermithid parasitism of A. axis and Chrysodeixis spp. along with its molecular characterization.

Application of 18S rDNA Clone Library to Detect Diatom Population Diversity in Dianchi.

Objective To detect the diatom population diversity in Dianchi by constructing a 18S rDNA clone library. Methods DNA from diatoms in 6 water samples of Dianchi was amplified with diatom 18S rDNA specific primer.The 18S rDNA clone library was constructed, and clones were randomly selected for sequence. Sequence alignment was performed by BLAST. The diatom population distribution in Dianchi was analyzed and the phylogenetic tree of diatom 18S rDNA in Dianchi waters was established with the MEGA v7.0.14 software. Results Two hundred and forty clones were sequenced, with 167 diatom sequences obtained, including 11 diatom species such as Stephanodiscus, Diatoma, and Melosira. There were certain differences in diatom population distribution among the 6 samples. Conclusion The population distribution of diatom species in Dianchi shows unique features and the sequence analysis of diatom 18S rDNA has a certain reference value to the inference of forensic drowning sites.

Fluorite Dissolution by a Phosphate-Solubilizing Bacterium Isolated from Groundwater of Xianghuangqi County, Inner Mongolia, China

Xianghuangqi County of Inner Mongolia is a typical high-fluoride area in China. Present work discussed a possible role of phosphate-solubilizing bacteria (PSBs) in the formation of high-fluoride groundwater in this area. An indigenous PSB was isolated from the local groundwater. Analysis of 16S rDNA sequence indicates that the bacterium belongs to the Pseudomonas genus. This bacterium caused acidification of the culture media under phosphate-limited conditions. HPLC analysis detected several metabolites that are likely to acidify the cultural media. Fluorite dissolution experiment with this bacterium in minimum medium containing 2 mg/L, 20 mg/L, and 200 mg/L glucose showed that the initial concentration of glucose has a large effect on pH of the culture medium and the fluorite dissolution rate. The pH of bacterial cell-free medium remained constant throughout the experiment. Introduction of the PSB caused an initial decrease in pH, followed by an increase. The measured pH minima were 4.8, 5.8, and 6.0 for culture media amended with 200 mg/L, 20 mg/L, and 2 mg/L glucose, respectively. A slow increase of the fluoride concentration in bacterial cell-free medium was observed, and inoculation of the PSB increased the rate of fluoride release causing the concentration of fluoride in bacterial-inoculated medium to markedly exceed that found in control medium. The highest fluorite dissolution rate was observed in culture medium amended with 200 mg/L glucose, while the rates observed in culture medium amended with 20 mg/L and 2 mg/L glucose were comparable. Given the ubiquity of PSBs in natural environment, these findings show PSBs could be important contributors to fluoride mobilization in high fluoride area.

Population genetic analysis of trematode Parasaccocoelium mugili Zhukov, 1971 (Haploporidae Nicoll, 1914) from the Russian Far East and Vietnam based on ribosomal ITS and mitochondrial COI gene partial sequence data.

Intraspecific variation of Parasaccocoelium mugili collected from mullet fish of the south of Russian Far East and Vietnam has previously been estimated on the basis of two molecular markers: ribosomal internal transcribed spacer 1 (ITS1) rDNA and mitochondrial cytochrome oxidase I (COI) gene sequences. In the present study, molecular identification of this species from the Kievka River, Primorye and from Vietnam was performed by analysis of 28S rDNA sequences. Analysis of ITS1 rDNA sequences variation revealed two highly differentiated main groups, representing trematode specimens from the two regions. Genetic variation within each region was relatively low. Mitochondrial COI gene sequence data analysis revealed fixed nucleotide and amino acid substitutions, and supported the existence of two genetically different groups associated with geographical origin. Analysis of the COI gene fragments showed extremely high variation within Russian and Vietnamese P. mugili samples. Our results for P. mugili most probably represent a case of initial step of allopotric speciation for this trematode, caused by living strategy of its definitive host at evolutionary scale. Mitochondrial DNA sequence data show that existence of gene flow between local populations of P. mugili in the Primorye Region caused by definitive hosts can be proposed.

Biodegradation of Atrazine by the Novel Klebsiella variicola Strain FH-1.

Bacterial strain FH-1 with high efficiency of degrading Atrazine is separated by means of enrichment culture from the soil applied with Atrazine for many years. FH-1, recognized as Klebsiella variicola based on phylogenetic analysis of 16S rDNA sequences, can grow with Atrazine which is the sole nitrogen source. In fluid inorganic salt medium, the optimal degradation temperature, pH value, and initial concentration of Atrazine are 25°C, 9.0, and 50 mg L–1, respectively, and the degradation rate of Atrazine by strain FH-1 reached 81.5% in 11 d of culture. The degrading process conforms to the kinetics equation of pesticide degradation. Among the metal ions tested, Zn2+ (0.2 mM) has the most significant effect of facilitation on the degradation of Atrazine. In the fluid medium with Zn2+, the degradation rate of Atrazine is increased to 72.5%, while the Cu2+ (0.2 mM) inhibits the degradation of Atrazine. The degradation products of Atrazine by strain FH-1 were identified as HEIT (2-hydroxyl-4-ethylamino-6-isopropylamino-1,3,5-triazine), MEET (2-hydroxyl-4,6-bis(ethylamino)-1,3,5-triazine), and AEEO (4,6-bis(ethylamino)-1,3,5-triazin-2(1H)-one) by HPLC-MS/MS. Three genes (atzC, trzN, and trzD) encoding for Atrazine degrading enzymes were identified by PCR and sequencing in strain FH-1. This study provides additional theoretical support for the application of strain FH-1 in bioremediation of fields polluted by Atrazine.

Dose Effects of Orally Administered Spirulina Suspension on Colonic Microbiota in Healthy Mice.

Oral supplemented nutraceuticals derived from food sources are surmised to improve the human health through interaction with the gastrointestinal bacteria. However, the lack of fundamental quality control and authoritative consensus (e.g., formulation, route of administration, dose, and dosage regimen) of these non-medical yet bioactive compounds are one of the main practical issues resulting in inconsistent individual responsiveness and confounded clinical outcomes of consuming nutraceuticals. Herein, we studied the dose effects of widely used food supplement, microalgae spirulina (Arthrospira platensis), on the colonic microbiota and physiological responses in healthy male Balb/c mice. Based on the analysis of 16s rDNA sequencing, compared to the saline-treated group, oral administration of spirulina once daily for 24 consecutive days altered the diversity, structure, and composition of colonic microbial community at the genus level. More importantly, the abundance of microbial taxa was markedly differentiated at the low (1.5 g/kg) and high (3.0 g/kg) dose of spirulina, among which the relative abundance of Clostridium XIVa, Desulfovibrio, Eubacterium, Barnesiella, Bacteroides, and Flavonifractor were modulated at various degrees. Evaluation of serum biomarkers in mice at the end of spirulina intervention showed reduced the oxidative stress and the blood lipid levels and increased the level of appetite controlling hormone leptin in a dose-response manner, which exhibited the significant correlation with differentially abundant microbiota taxa in the cecum. These findings provide direct evidences of dose-related modulation of gut microbiota and physiological states by spirulina, engendering its future mechanistic investigation of spirulina as potential sources of prebiotics for beneficial health effects via the interaction with gut microbiota.

Numerical analysis of phenotypic properties, genomic fingerprinting, and multilocus sequence analysis of Bradyrhizobium strains isolated from root nodules of Lembotropis nigricans of the tribe Genisteae

PurposeThe aim of this study was to estimate the level of genomic and phenotypic diversity as well as the genus and species position of bacterial strains isolated from root nodules of Lembotropis nigricans (family Fabaceae).MethodsThe genomic diversity of studied L. nigricans nodule symbionts was examined by using BOX-PCR and AFLP (amplified fragment length polymorphism) fingerprinting techniques. To assign bacteria to the genus, numerical analysis of phenotypic features and comparative analysis of 16S rDNA sequences were performed. The comparative analysis of combined atpD, dnaK, gyrB, and rpoB gene sequences (multilocus sequence analysis, MLSA) was used to determine the most closely related species to the studied bacteria.ResultsBoth BOX-PCR and AFLP techniques revealed a high level of genomic heterogeneity of L. nigricans nodulators. Among 33 studied bacteria, 32 genotypes were delineated by the AFLP method and 27 genotypes were identified by the BOX-PCR fingerprinting. The numerical analysis of 86 phenotypic characteristics of L. nigricans nodule isolates and reference rhizobia showed that studied bacteria belong to the genus Bradyrhizobium. Affiliation of L. nigricans nodule isolates to the genus Bradyrhizobium was supported by comparative analysis of 16S rDNA sequences and the concatenation of atpD, dnaK, gyrB, and rpoB gene sequences. MLSA indicated also that L. nigricans microsymbionts are members of Bradyrhizobium japonicum.ConclusionL. nigricans root nodule symbionts are members of Bradyrhizobium japonicum and exhibit high phenotypic and genomic diversity important for their survival in soil.

Phylogenetic insights into the diversity of Chryseobacterium species.

The genus Chryseobacterium was formally established in 1994 and contains 112 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin-type pigment. The genomes of 83 of these 112 species have been sequenced in view of their importance in clinical microbiology and potential applications in biotechnology. The National Center for Biotechnology Information taxonomy browser lists 1415 strains as members of the genus Chryseobacterium , of which the genomes of 94 strains have been sequenced. In this study, by comparing the 16S rDNA and the deduced proteome sequences, at least 20 of these strains have been proposed to represent novel species of the genus Chryseobacterium . Furthermore, a yellow-coloured bacterium isolated from dry soil in the USA (and identified as Flavobacterium sp. strain B-14859) has also been reconciled as a novel member of the genus Chryseobacterium based on the analysis of 16S rDNA sequences and the presence of flexirubin. Yet another bacterium (isolated from a water sample collected in the Western Ghats of India and identified as Chryseobacterium sp. strain WG4) was also found to represent a novel species. These proposals need to be validated using polyphasic taxonomic approaches.