scholarly journals Diverse thermophilic Bacillus species with multiple biotechnological activities are associated within the Egyptian soil and compost samples

2021 ◽  
Vol 104 (4) ◽  
pp. 003685042110552
Author(s):  
SA Zalma ◽  
WM El-Sharoud
Keyword(s):  
Biological Diversity ◽  
16S Rrna Gene Sequencing ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Thermophilic Bacillus ◽  
Genetic Groups ◽  
Mixing Rates ◽  
Egyptian Soil ◽  
Rrna Gene Sequencing ◽  
High Degree

Thermophilic strains of Bacillus can express enzymes of higher thermal stability, which allows carrying out industrial fermentations under higher temperatures. This lowers the contamination potential, accelerates mixing rates and facilitates the recovery of fermentation end products. The present study was thus designed to isolate and characterize thermophilic Bacillus cultures from soil and compost samples. Forty-two thermophilic Bacillus isolates could be identified employing morphological, physiological and the 16S rRNA gene sequencing analyses. The isolates showed a high degree of biological diversity involving 13 Bacillus species and 1 subspecies but were dominated by Bacillus licheniformis. Phylogenetic analysis of B. licheniformis isolates based on the DNA sequencing of gyrA and rpoB genes presented them in two main genetic groups. Isolates of five thermophilic species including B. licheniformis, Bacillus altitudinis, Bacillus paralicheniformis, Bacillus subtilis and Bacillus thermoamylovorans showed multiple activities to degrade all of cellulose, hemicellulose and lignin. Those multifunctional thermophilic Bacillus isolates can be harnessed in the degradation of plant wastes for the production of biofuels and compost.

scholarly journals Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk

2004 ◽  
Vol 54 (3) ◽  
pp. 885-891 ◽  
Author(s):  
Patsy Scheldeman ◽  
Karen Goossens ◽  
Marina Rodriguez-Diaz ◽  
Annelies Pil ◽  
Johan Goris ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dairy Farm ◽  
16S Rrna Gene Sequencing ◽  
Raw Milk ◽  
Rrna Gene ◽  
Heat Treated ◽  
Dairy Plant ◽  
Rrna Gene Sequencing ◽  
High Degree

Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified as Bacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genus Paenibacillus, with Paenibacillus lautus as the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA–DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C15 : 0, C16 : 0 and iso-C15 : 0 were among the major fatty acids and the genomic DNA G+C content was 51·6–51·7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genus Paenibacillus as Paenibacillus lactis sp. nov. The type strain is MB 1871T (=LMG 21940T=DSM 15596T).

scholarly journals Isolation and characterization of Bacillus spp. strains as potential probiotics for poultry

2019 ◽  
Vol 65 (10) ◽  
pp. 762-774 ◽  
Author(s):  
Alejandro Penaloza-Vazquez ◽  
Li Maria Ma ◽  
Patricia Rayas-Duarte
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Antibiotic Use ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Broiler Chicks ◽  
Long Term Stability ◽  
Isolation And Characterization ◽  
Sporulation Efficiency ◽  
Bacillus Spp ◽  
Rrna Gene Sequencing

Probiotics have become one of the potential solutions to global restriction on antibiotic use in food animal production. Bacillus species have been attractive probiotics partially due to their long-term stability during storage. In this study, 200 endospore-forming bacteria isolates were recovered from sourdough and the gastrointestinal tract (GIT) of young broiler chicks. Based on the production of a series of exoenzymes and survivability under stress conditions similar to those in the poultry GIT, 42 isolates were selected and identified by 16S rRNA gene sequencing. Seven strains with a profile of high enzymatic activities were further evaluated for sporulation efficiency, biofilm formation, compatibility among themselves (Bacillus spp.), and antagonistic effects against three bacteria pathogenic to poultry and humans: Enterococcus cecorum, Salmonella enterica, and Shiga-toxin-producing Escherichia coli. The strains from sourdough were identified as Bacillus amyloliquefaciens whereas the ones from the chicks’ GIT were Bacillus subtilis. These strains demonstrated remarkable potential as probiotics for poultry.

scholarly journals Screening of Potent Arsenic Resistant and Plant Growth Promoting Bacillus species from the Soil of Terai Region of Nepal

2019 ◽  
Vol 6 ◽  
pp. 1-9
Author(s):  
Pramod Poudel ◽  
Ashish Nepal ◽  
Rashmi Roka Magar ◽  
Pratibha Rauniyar ◽  
Lil Buda Magar
Keyword(s):  
Plant Growth ◽  
Sodium Arsenite ◽  
16S Rrna Gene Sequencing ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Sodium Arsenate ◽  
Bacillus Spp ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Rrna Gene Sequencing

Objectives: To isolate arsenic resistant Bacillus spp. and to determine plant growth promoting activities.  Methods: Eighteen soil samples were collected from the agricultural soil of Terai region of Nepal. Selective isolation of Bacillus species was done by heating the soil at 80 ºC for 15 minutes before the isolation. Nutrient agar was used as an isolation medium. Screening of arsenic resistant Bacillus species was done using nutrient agar supplemented with 100 ppm sodium arsenate and sodium arsenite. For plant growth promoting activity; IAA production was detected taking 0.1% tryptophane and measuring absorbance at 540 nm, NH3 production was tested by Nessler’s reagent and phosphate solubilization activity was detected by growing colonies on Pikovskaya’s agar. Sugar assimilation test was performed to identify the isolates. Most potent arsenic resistant isolate was identified by 16S rRNA gene sequencing. Results: Among 54 randomly selected isolates, 42 were found to be Gram-positive rod-shaped, spore-forming while 12 isolates were Gram-negative bacteria. The isolates IN12a, M12a and BG34a showed growth on 100 ppm sodium arsenite containing NA. Only isolate M12a tolerated up to 1000 ppm and 15000 ppm of sodium arsenite and sodium arsenate respectively, while other isolates could not grow above 400 ppm sodium arsenite. The isolates IN12a and M12a were able to produce IAA and solubilize phosphate while BG34a could not. Both the isolates IN12a and M12a were able to utilize the sugars glucose, fructose, lactose, sucrose, galactose, mannose, mannitol, maltose and xylose.  Based on the 16S rRNA gene sequencing, isolate M12a was identified to be Bacillus flexus with highest similarity of 99.2%. Conclusion: Arsenic resistant and plant growth promoting Bacillus spp. was isolated from the agricultural soil of Terai region of Nepal

Screening of cattle gut associated Bacillus strains for their potential use as animal probiotic

2018 ◽  
Author(s):  
M. Naeem ◽  
I. Ahmed ◽  
S. Ahmed ◽  
Z. Ahmed ◽  
M. N. Riaz ◽  
...  
Keyword(s):  
Animal Feed ◽  
Survival Rates ◽  
Significant Risk ◽  
16S Rrna Gene Sequencing ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Promising Alternative ◽  
Probiotic Potential ◽  
Rrna Gene Sequencing ◽  
Animal Diet

Use of antibiotic in animal feed pose a significant risk to human health. Over the last decade uses of probiotics increasingly viewed as an alternative to antibiotic. Bacillus are currently being used as feed supplements in animal diet, due to their enhanced tolerance rate and survivability under harsh gut environment. Animal gut is a rich source for Bacillus species isolation. There is still a scarcity of information on the Bacillus species of livestock species. The present study was carried out to identify Bacillus species from animal gut to evaluate their probiotic potential. Three (NCCP-2004a, NCCP-2029 and NCCP-2029) strains were selected as putative probiotics strains based on their super acid and bile survival rates. These isolates were identified as Bacillus subtilis subsp. inaquosorum (NCCP-2029, NCCP-2025). Bacillus tequilensis (NCCP-2004a) by 16S rRNA gene sequencing. NCCP-2004a elicited best results regarding antimicrobial potential and its ability to survive on acid and bile conditions. The results of present study demonstrated that the B. tequilensis showed a promising alternative probiotic candidate to the use of antibiotics in the dairy feeding system.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

scholarly journals The growth response of rice (Oryza sativa L. var. FARO 44) in vitro after inoculation with bacterial isolates from a typical ferruginous ultisol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Musa Saheed Ibrahim ◽  
Beckley Ikhajiagbe
Keyword(s):  
16S Rrna ◽  
Bacillus Cereus ◽  
Proteus Mirabilis ◽  
Growth Response ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rice Seedlings ◽  
Rrna Gene Sequencing

Abstract Background Rice forms a significant portion of food consumed in most household worldwide. Rice production has been hampered by soil factors such as ferruginousity which has limited phosphorus availability; an important mineral component for the growth and yield of rice. The presence of phosphate-solubilizing bacteria (PSB) in soils has been reported to enhance phosphate availability. In view of this, the present study employed three bacteria species (BCAC2, EMBF2 and BCAF1) that were previously isolated and proved P solubilization capacities as inocula to investigate the growth response of rice germinants in an in vitro setup. The bacteria isolates were first identified using 16S rRNA gene sequencing and then applied as inoculum. The inolula were prepared in three concentrations (10, 7.5 and 5.0 ml) following McFarland standard. Viable rice (var. FARO 44) seeds were sown in petri dishes and then inoculated with the three inocula at the different concentrations. The setup was studied for 28 days. Results 16S rRNA gene sequencing identified the isolates as: isolate BCAC2= Bacillus cereus strain GGBSU-1, isolate BCAF1= Proteus mirabilis strain TL14-1 and isolate EMBF2= Klebsiella variicola strain AUH-KAM-9. Significant improvement in rice germination, morphology, physiology and biomass parameters in the bacteria-inoculated setups was observed compared to the control. Germination percentage after 4 days was 100 % in the inoculated rice germinants compared to 65% in the control (NiS). Similarly, inoculation with the test isolates enhanced water-use efficiency by over 40%. The rice seedlings inoculated with Bacillus cereus strain GGBSU-1 (BiS) showed no signs of chlorosis and necrosis throughout the study period as against those inoculated with Proteus mirabilis strain TL14-1 (PiS) and Klebsiella variicola strain AUH-KAM-9 (KiS). Significant increase in chlorophyll-a, chlorophyll-b and alpha amylase was observed in the rice seedlings inoculated with BiS as against the NiS. Conclusion Inoculating rice seeds with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 in an in vitro media significantly improved growth parameters of the test plant. Bacillus cereus strain GGBSU-1 showed higher efficiency due to a more improved growth properties observed.

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