Publications

development of a systematic feedback isolation approach for targeted strains from mixed culture systems.	elucidation of functions of bacteria in a mixed culture system (mcs) such as composting, activated sludge system is difficult, since the system is complicating with many unisolated bacteria. here, we developed a systematic feedback isolation strategy for the isolation and rapid screening of multiple targeted strains from mcs. six major strains (corynebacterium sphenisci, bacillus thermocloacae, bacillus thermoamylovorans, bacillus smithii, bacillus humi, and bacillus coagulans), which are detect ...	2017	27570222
efficient genome editing of a facultative thermophile using mesophilic spcas9.	well-developed genetic tools for thermophilic microorganisms are scarce, despite their industrial and scientific relevance. whereas highly efficient crispr/cas9-based genome editing is on the rise in prokaryotes, it has never been employed in a thermophile. here, we apply streptococcus pyogenes cas9 (spcas9)-based genome editing to a moderate thermophile, i.e., bacillus smithii, including a gene deletion, gene knockout via insertion of premature stop codons, and gene insertion. we show that spca ...	2017	28146359
complete genome sequence of thermophilic bacillus smithii type strain dsm 4216(t).	bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. we determined the complete genomic sequence of the b. smithii type strain dsm 4216(t), which consists of a 3,368,778 bp chromosome (genbank accession number cp012024.1) and a 12,514 bp plasmid (genbank accession ...	2016	27559429
isolation and screening of thermophilic bacilli from compost for electrotransformation and fermentation: characterization of bacillus smithii et 138 as a new biocatalyst.	thermophilic bacteria are regarded as attractive production organisms for cost-efficient conversion of renewable resources to green chemicals, but their genetic accessibility is a major bottleneck in developing them into versatile platform organisms. in this study, we aimed to isolate thermophilic, facultatively anaerobic bacilli that are genetically accessible and have potential as platform organisms. from compost, we isolated 267 strains that produced acids from c5 and c6 sugars at temperature ...	2015	25556192
establishment of markerless gene deletion tools in thermophilic bacillus smithii and construction of multiple mutant strains.	microbial conversion of biomass to fuels or chemicals is an attractive alternative for fossil-based fuels and chemicals. thermophilic microorganisms have several operational advantages as a production host over mesophilic organisms, such as low cooling costs, reduced contamination risks and a process temperature matching that of commercial hydrolytic enzymes, enabling simultaneous saccharification and fermentation at higher efficiencies and with less enzymes. however, genetic tools for biotechno ...	2015	26148486
large fragment of dna polymerase i from geobacillus sp. 777: cloning and comparison with dna polymerases i in practical applications.	a truncated gene of dna polymerase i from the thermophilic bacteria geobacillus sp. 777 encoding a large fragment of enzyme (lf gss pol) was cloned and sequenced. the resulting sequence is 1776-bp long and encodes a 592 aa protein with a predicted molecular mass of 69.8 kda. enzyme was overexpressed in e. coli, purified by metal-chelate chromatography, and biochemically characterized. the specific activity of lf gss pol is 104,000 u/mg (one unit of enzyme was defined as the amount of enzyme that ...	2015	26289299
exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting.	the composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. this work analyzes the identity of microbial community that persists throughout lignocellulose-based composting, evaluates their metabolic activities and studies the capability of selected isolates for composting bioaugmentation. bacterial species of the phyla firmicutes, actinobacteria and proteobacteria and fungi of the phylum ascomycota were ubiquitous throughout the composting. ...	2014	24759645
bioprocess development for nicotinic acid hydroxamate synthesis by acyltransferase activity of bacillus smithii strain iitr6b2.	in this work, acyltransferase activity of a new bacterial isolate bacillus smithii strain iitr6b2 was utilized for the synthesis of nicotinic acid hydroxamate (nah), a heterocyclic class of hydroxamic acid. nah is an important pyridine derivative and has found its role as bioligand, urease inhibitor, antityrosinase, antioxidant, antimetastatic, and vasodilating agents. amidase having acyltransferase activity with nicotinamide is suitable for nicotinic acid hydroxamate production. however, amidas ...	2013	23794117
characterization of aerobic spore-forming bacteria associated with industrial dairy processing environments and product spoilage.	due to changes in the design of industrial food processing and increasing international trade, highly thermoresistant spore-forming bacteria are an emerging problem in food production. minimally processed foods and products with extended shelf life, such as milk products, are at special risk for contamination and subsequent product damages, but information about origin and food quality related properties of highly heat-resistant spore-formers is still limited. therefore, the aim of this study wa ...	2013	23973839
detergent compatible alkaline lipase produced by marine bacillus smithii btms 11.	bacillus smithii btms 11, isolated from marine sediment, produced alkaline and thermostable lipase. the enzyme was purified to homogeneity by ammonium sulfate precipitation and ion exchange chromatography which resulted in 0.51 % final yield and a 4.33 fold of purification. the purified enzyme was found to have a specific activity of 360 iu/mg protein. sds-page analyses, under non-reducing and reducing conditions, yielded a single band of 45 kda indicating the single polypeptide nature of the en ...	2013	23443894
Isolation and characterization of aerobic culturable arsenic-resistant bacteria from surfacewater and groundwater of Rautahat District, Nepal.	Arsenic (As) contamination of groundwater is a serious Environmental Health Management issue of drinking water sources especially in Terai region of Nepal. Many studies have reported that due to natural abundance of arsenic in the environment, various bacteria have developed different resistance mechanisms for arsenic compound. In this study, the culturable arsenic-resistant bacteria indigenous to surfacewater as well as groundwater from Rautahat District of Nepal were randomly isolated by stand ...	2011	21868146
identification of thermophilic bacterial strains producing thermotolerant hydrolytic enzymes from manure compost.	ten thermophilic bacterial strains were isolated from manure compost. phylogenetic analysis based on 16s rrna genes and biochemical characterization allowed identification of four different species belonging to four genera: geobacillus thermodenitrificans, bacillus smithii, ureibacillus suwonensis and aneurinibacillus thermoaerophilus. pcr-rflp profiles of the 16s-its-23s rrna region allowed us to distinguish two subgroups among the g. thermodenitrificans isolates. isolates were screened for the ...	2011	23448754
protective effect by bacillus smithii tbmi12 spores of salmonella serotype enteritidis in mice.	avoiding food-borne diseases by competitive exclusion agents is a proactive strategy. in the current paper, we report the use of bacillus smithii tbmi12 spores as potential competitive exclusion agents. one group of mice was predosed for three successive days with 10(8) colony forming units of b. smithii tbmi12 spores followed by inoculation with 10(6) colony forming units of wild-type salmonella enterica serotype enteritidis cells. microbial plate counts of the animals' livers and spleens showe ...	2010	21840796
characterization of thermo-stable endoinulinase from a new strain bacillus smithii t7.	a new thermophilic inulinase-producing strain, which grows optimally at 60 degrees c, was isolated from soil samples with medium containing inulin as a sole carbon source. it was identified as a bacillus smithii by analysis of 16s rdna. maximum inulinase yield of 135.2 iu/ml was achieved with medium ph7.0, containing inulin 2.0%, (nh(4))h(2)po(4) 0.5%, yeast extract 0.5%, at 50 degrees c 200 rpm shaker for 72-h incubation. the purified inulinase from the extracellular extract of b. smithii t7 sh ...	2009	18663416
the microbial-kill characteristics of saturated steam plus 1,000 to 10,000 ppm hydrogen peroxide at atmospheric pressure.	this is the report of a project carried out to determine the microbial-kill characteristics of saturated steam plus hydrogen peroxide (h2o2) using a specially-constructed test apparatus. spores on stainless-steel planchets were inserted into a flowing gaseous atmosphere of steam plus h2o2 for a timed exposure to the lethal agent. the specially-designed test apparatus and its operating parameters are described. geobacillus stearothermophilus (former name, bacillus stearothermophilus) spore-death ...	2008	18540535
caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in china.	a thermophilic, alkaliphilic and catalase-positive bacterium, designated strain ha6(t), was isolated from a hot spring in china. the strain was aerobic and chemo-organotrophic and grew optimally at 60 degrees c, ph 8.5 and 1.5 % (w/v) nacl. the cells were gram-positive rods, forming single terminal endospores. the predominant cellular fatty acids were iso-c(15 : 0) and iso-c(17 : 0). the cell-wall peptidoglycan contained meso-diaminopimelic acid. the genomic dna g+c content was 45.2 mol%. phylog ...	2006	16738094
bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the ayu trough.	two thermophilic, spore-forming strains, tm1(t) and tm5, were isolated from deep-sea sediment (4000 m below sea level) of the ayu trough in the western pacific ocean. cells of the two strains were gram-positive, motile and rod-shaped. their spores were ellipsoidal, subterminal to terminal and occurred in swollen sporangia. the two strains grew at temperatures up to 65 degrees c and in the ph range 6.5-9.0. the nacl concentration for optimal growth was 3.0 % (w/v) and growth was inhibited by 5 % ...	2005	15879257
cloning, purification, crystallization and preliminary x-ray diffraction analysis of nitrile hydratase from the themophilic bacillus smithii sc-j05-1.	nitrile hydratase (nhase) converts nitriles to the corresponding amides and is recognized as having important industrial applications. purification, cloning, crystallization and initial crystallographic studies of the nhase from bacillus smithii sc-j05-1 (bs nhase) were conducted to analyze the activity, specificity and thermal stability of this hydrolytic enzyme. bs nhase was purified to homogeneity from microbial cells of b. smithii sc-j05-1 and the nucleotide sequences of both the alpha- and ...	2005	16511211
evaluating the formulae for integrated lethality in ethylene oxide sterilization using six different endospore forming strains of bacteria, and comparisons of integrated lethality for ethylene oxide and steam systems.	bacterial endospores from six different species of bacteria were exposed to a spectrum of ethylene oxide (eto) sterilizing conditions. temperature was varied from 40 to 60 degrees c and the ethylene oxide concentration was varied from 300 to 750 mg/l. relative humidity was maintained at 60+/-10% rh. the fraction negative procedure was used to determine the d value for each of the test conditions. bacterial species tested included bacillus atrophaeus atcc # 9372, bacillus smithii atcc # 51232, ba ...	2005	15796136
crystal structure of nitrile hydratase from a thermophilic bacillus smithii.	the crystal structure of the nitrile hydratase (nhase) from bacillus smithii sc-j05-1 was determined. our analysis of the structure shows that some residues that seem to be responsible for substrate recognition are different from those of other nhases. in particular, the phe52 in the beta subunit of nhase from b. smithii covers the metal center partially like a small lid and narrows the active site cleft. it is well known that the nhase from b. smithii especially prefers aliphatic nitriles for i ...	2003	14637142
purification and partial characterization of bacillocin 490, a novel bacteriocin produced by a thermophilic strain of bacillus licheniformis.	background: applications of bacteriocins as food preservatives have been so far limited, principally because of their low antimicrobial activity in foods. nisin is the only bacteriocin of significant use, but applications are restricted principally because of its very low activity at neutral or alkaline ph. thus the isolation of new bacteriocins active in foods is desirable. results: we isolated a bacillus licheniformis thermophilic strain producing a bacteriocin with some novel features, named ...	2002	12076356
isolation of a thermophilic poly-l-lactide degrading bacterium from compost and its enzymatic characterization.	thermophilic poly-l-lactide-degrading bacteria were isolated from a garbage fermentor. one of the isolates, strain pl21, was identified as bacillus smithii based on its physiological properties, sugar assimilation pattern, and partial 16s rdna sequence. the degradation activity of poly-l-lactide exibited by the culture fluid was parallel to the esterase activity, and the purified enzyme was active against various fatty acid esters and poly-l-lactide, at 60 degrees c and ph 5.	2001	16233100
factors affecting the production of nitrile hydratase by thermophilic bacillus smithii sc-j05-1.	ammonium present in the medium was found to control the production of nitrile hydratases (nhase) by a moderate thermophile, bacillus smithii sc-j05-1. the enzyme production is initiated in the absence of ammonium and suppressed in the presence of ammonium. in addition to cobalt ions as the coordinated metal ion, manganese ions are also required for nhase production.	2000	16232745
the phylogenetic diversity of thermophilic members of the genus bacillus as revealed by 16s rdna analysis.	sixteen thermophilic strains of the genus bacillus, representing eight validly described and six invalidly described species, as well as one unassigned strain, were investigated by comparative 16s rdna analyses and the sequences compared to the existing database for the genera bacillus and alicyclobacillus. the majority of strains were found to cluster in two groups represented by b. stearothermophilus and b. pallidus. bacillus smithii, b. thermocloacae, and b. thermoruber are phylogenetically w ...	1994	8138135
sequence of the gene encoding an alkaline serine protease of thermophilic bacillus smithii.	the complete nucleotide sequence of the gene encoding an alkaline serine protease from bacillus smithii has been determined. degenerate oligodeoxyribonucleotide primers were used to prime the amplification of a 507-bp sequence of the gene. this sequence was successively used for constructing new primers applied in inverse polymerase chain reaction, using as template self-ligated dna fragments. the deduced amino-acid sequence is compared to serine proteases from b. amyloliquefaciens, b. lichenifo ...	1994	8045417
numerical analysis and dna base compositions of some thermophilic bacillus species.	morphological, physiological, and biochemical characteristics and the dna base compositions of 133 thermophilic bacillus strains were determined. a total of 54 of these strains were received as identified species (mainly bacillus stearothermophilus, bacillus coagulans, bacillus brevis, and bacillus licheniformis) from international culture collections, and 79 newly isolated strains, which were isolated mainly from sugar diffusion juices of italian plants, were also examined. numerical taxonomy t ...	1991	1742196