Project description:"Leucobacter massiliensis" strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. "Leucobacter massiliensis" is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.
Project description:Bioflocculants are secondary metabolites produced by microorganisms during their growth which have received attentions due to their biodegradability, innocuousness and lack of secondary pollution from degradation intermediates. This study reports on a bioflocculant produced by Bacillus specie isolated from Thyume River in South Africa. The bacterial isolate was identified through 16S rDNA sequencing and the BLAST analysis of the nucleotide sequences revealed 99% similarity to Bacillus sp. BCT-7112. The sequence was subsequently deposited in the GenBank as Bacillus sp. AEMREG4 with accession number KP406729. The optimum culture conditions for bioflocculant production were an inoculum size 4% (v/v) (80%) and starch (81%) as well as yeast extract (82%) as sole carbon and nitrogen sources, respectively. Addition of Ca2+ greatly enhanced the flocculating activity (76%) of crude bioflocculant over a wide range of pH 4-10 and retained high flocculating activity when heated at 100 °C for 1 h. Chemical analyses of the purified bioflocculant revealed carbohydrate (79% w/w) as a predominant component followed by uronic acid (15% w/w) and protein (5% w/w). Fourier transform infrared spectrum revealed the presence of carboxyl, hydroxyl and methoxyl groups as the functional groups responsible for flocculation and the high flocculation activity achieved portends its industrial applicability.
Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature. Overall design: Here we have performed 36 microarrays and because channels were analyzed separately we have uploaded channels separately. We used six biological replicates of C. elegans grown in four bacterial environments (E. coli OP50, Micrococcus luteus, Bacillus megaterium, and Pseudomonas sp.). For each of those biological replicates we have performed three technical replicates because we made all six pair-wise comparisons amoungst the four bacterial environments. Dye swaps were performed. > Biological replicates (technical replicates) < Micrococcus luteus 1 (GSM399039,GSM399094,GSM399119) Micrococcus luteus 2 (GSM399426,GSM399431,GSM399459) Micrococcus luteus 3 (GSM399467,GSM399482,GSM399486) Micrococcus luteus 4 (GSM399489,GSM399493,GSM399500) Micrococcus luteus 5 (GSM399514,GSM399533,GSM399534) Micrococcus luteus 6 (GSM399539,GSM399544,GSM399547) E. coli OP50 1 (GSM399108,GSM399118,GSM399125) E. coli OP50 2 (GSM399427,GSM399428,GSM399465) E. coli OP50 3 (GSM399480,GSM399485,GSM399487) E. coli OP50 4 (GSM399490,GSM399492,GSM399495) E. coli OP50 5 (GSM399510,GSM399513,GSM399535) E. coli OP50 6 (GSM399541,GSM399542,GSM399546) Bacillus megaterium 1 (GSM399089,GSM399097,GSM399123) Bacillus megaterium 2 (GSM399429,GSM399437,GSM399458) Bacillus megaterium 3 (GSM399468,GSM399479,GSM399484) Bacillus megaterium 4 (GSM399496,GSM399498,GSM399505) Bacillus megaterium 5 (GSM399512,GSM399531,GSM399536) Bacillus megaterium 6 (GSM399538,GSM399543,GSM399549) Pseudomonas sp. 1 (GSM399029,GSM399082,GSM399113) Pseudomonas sp. 2 (GSM399432,GSM399457,GSM399464) Pseudomonas sp. 3 (GSM399481,GSM399483,GSM399488) Pseudomonas sp. 4 (GSM399491,GSM399494,GSM399509) Pseudomonas sp. 5 (GSM399511,GSM399532,GSM399537) Pseudomonas sp. 6 (GSM399540,GSM399545,GSM399548)
Project description:<p>Gut microbiota modulation by a probiotic is a novel therapy for hypercholesterolemia mitigation. This study initially investigated the potential hypocholesterolemic effect of Bacillus sp. DU-106 in hypercholesterolemic rats and explored its potential relation with gut microbiota. Sprague-Dawley rats received a high-fat diet, or a high-fat diet supplemented with 7.5 × 10<sup>9</sup> and 1.5 × 10<sup>10</sup> CFU/kg bw/day Bacillus sp. DU-106 (low-dose and high-dose groups). At the end of 9 weeks, Bacillus sp. DU-106 treatment significantly decreased the body weight, liver index, and total cholesterol. 16S rRNA sequencing showed that Bacillus sp. DU-106 intervention significantly increased bacterial richness and particularly increased the genus abundance of Turicibacter, Acinetobacter, Brevundimonas, and Bacillus and significantly decreased the abundance of Ralstonia. Metabolomic data further indicated that the supplementation of Bacillus sp. DU-106 remarkably changed the gut metabolic profiles of hypercholesterolemic rats and, in particular, elevated the metabolites of indole-3-acetate, methylsuccinic acid, creatine, glutamic acid, threonine, lysine, ascorbic acid, and pyridoxamine. Spearman's correlation analysis showed the close relation between the different genera and metabolites. In conclusion, Bacillus sp. DU-106 supplement ameliorated high-fat diet-induced hypercholesterolemia and showed potential probiotic benefits for the intestine.</p><p><strong>KEY POINTS:</strong> • A novel potential probiotic Bacillus sp. DU-106 ameliorated hypercholesterolemia in rats. • Bacillus sp. DU-106 supplement regulated gut microbiome structure and richness. • Bacillus sp. DU-106 supplement changed metabolic profiles in high-fat diet rats. • Significant correlations were observed between differential genera and metabolites.</p>
Project description:We report the draft genome sequences of Bacillus glennii V44-8, Bacillus saganii V47-23a, and Bacillus sp. strain V59.32b, isolated from the Viking spacecraft assembly cleanroom, and Bacillus sp. strain MER_TA_151 and Paenibacillus sp. strain MER_111, isolated from the Mars Exploration Rover (MER) assembly cleanroom.
Project description:BACKGROUND:Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. RESULTS:Here, we identified a 5,436,472?bp chromosome with 40.30% GC content and a 241,339?bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated. CONCLUSIONS:The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.
Project description:We present the draft genome sequence for Bacillus sp. strain PF3, Bacillus sp. strain K6W, Cellulomonas sp. strain B12, Cellulomonas sp. strain K38, Cellulomonas sp. strain K39, and Cellulomonas sp. strain K42B. These bacteria were isolated from contaminated soils, and their genomes contain genes related to chromate transport and reduction.
Project description:To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.
Project description:Here, we report the draft genome sequences of Bacillus subtilis A1, Sphingobacterium sp. strain A3, and Pseudomonas sp. strain A29; Sphingobacterium sp. A3 and Pseudomonas sp. A29 were identified as Bacillus velezensis strain A3 and Bacillus subtilis strain A29, respectively, after a quality control check of the whole-genome sequences deposited in the NCBI database. These bacteria exhibit tremendous production of siderophores and significant antimicrobial potential. When inoculated on maize, these isolates increase its yield.