A microcomputer program for establishing and maintaining a database for laboratory culture collections

A computer program that facilitates the creation of a culture collection database has been written for a microcomputer (Apple He with a Z-80 card) using dBASE II® (Ashton-Tate). The Culture Collection Program accommodates up to 250 individual strain records on one 5 1/4" floppy disk. For each strain, information that can be stored includes the name of the micro-organism, culture collection number, antibiotic resistance markers, plasmids, genetic markers, references, growth medium, growth temperature and additional comments. The last date of subculturing can be ascertained and information about the status of the preserved cultures can also be noted. With a menu-driven format which requires no computer programming expertise, the user can readily create new entries, update old ones and search the database for strains with certain common properties.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

A microcomputer-based information storage and retrieval system for the maintenance of records for a culture collection

A microcomputer-based system for the storage and retrieval of information on strains in a culture collection is described. The system was designed around commercially available software packages written for microcomputers. Two additional programs were written using the BASIC language to allow a catalogue of the culture collection to be printed in a specific format. The details of each strain in the collection were stored on a floppy disc. Details of new strains were added to this database and information relating to existing cultures was modified or, where necessary, deleted from the collection. The database can be searched to supply details of a particular culture or to identify those cultures which possess certain attributes. The records for the whole collection were sorted alphabetically by species name, and numerically by accession number, and a word-processing package was used to print a catalogue of the culture collection.     

Screening and characterization of butanol‐tolerant micro‐organisms

Aims: Poor butanol tolerance of solventogenic stains directly limits their butanol production during industrial‐scale fermentation process. This study was performed to search for micro‐organisms possessing elevated tolerance to butanol. Methods and Results: Two strains, which displayed higher butanol tolerance compared to commonly used solventogenic Clostridium acetobutylicum, were isolated by evolution and screening strategies. Both strains were identified as lactic acid bacteria (LAB). On this basis, a LAB culture collection was tested for butanol tolerance, and 60% of the strains could grow at a butanol concentration of 2·5% (v/v). In addition, an isolated strain with superior butanol tolerance was transformed using a certain plasmid. Conclusions: The results indicate that many strains of LAB possessed inherent tolerance of butanol. Significance and Impact of the Study: This study suggests that LAB strains may be capable of producing butanol to elevated levels following suitable genetic manipulation.     

Yeast culture collections of the world: meeting the needs of industrial researchers

The importance of selecting optimal yeast strains for research or industrial applications is often underestimated. For example, utilizing a strain background that already provides the desired stress tolerance or nutrient utilization profile can eliminate costly strain optimization. Yeast culture collections can provide not only the yeast strains but also data and curator expertise to help narrow the search for the optimal strain. While some collections are known for a broad range of cultures and services, other "boutique" collections can provide a broader selection of strains of certain categories, a surprising amount of characterization data, and assistance in selecting strains. This article provides information on dozens of yeast collections of the world, profiles of selected yeast culture collections, and the services that they provide: e.g., strain preservation for patent or safe deposit purposes, species identification service, training workshops, and consulting on yeast identification and physiology. Utilization of these services can save industrial researchers valuable time and resources.     

Purification and characterisation of an ester hydrolase from a strain of Arthrobacter species: its application in asymmetrisation of 2-benzyl-1,3-propanediol acylates

An ester hydrolase (ABL) has been isolated from a strain of Arthrobacter species (RRLJ-1/95) maintained in the culture collection of this laboratory. The purified enzyme has a specific activity of 1700 U/mg protein and is found to be composed of a single subunit (Mr 32,000), exhibiting both lipase and esterase activities shown by hydrolysis of triglycerides and p-nitrophenyl acetate respectively. Potential application of the enzyme concerns the asymmetrisation of prochiral 2-benzyl-1,3-propanediol esters besides enantioselective hydrolysis of alkyl esters of unsubstituted and substituted 1-phenyl ethanols.     

Marinobacterium sp. strain DMS-S1 uses dimethyl sulphide as a sulphur source after light-dependent transformation by excreted flavins

Marinobacterium sp. strain DMS-S1 is a unique marine bacterium that can use dimethyl sulphide (DMS) as a sulphur source only in the presence of light. High-performance liquid chromatography (HPLC) analyses of the culture supernatant revealed that excreted factors, which could transform DMS to dimethyl sulphoxide (DMSO) under light, are FAD and riboflavin. In addition, FAD appeared to catalyse the photolysis of DMS to not only DMSO but also methanesulphonate (MSA), formate, formaldehyde and sulphate. As strain DMS-S1 can use sulphate and MSA as a sole sulphur source independently of light, the excretion of flavins appeared to support the growth on DMS under light. Furthermore, three out of 12 marine bacteria from IAM culture collection were found to be able to grow on DMS with the aid of photolysis by the flavins excreted. This is the first report that bacteria can use light to assimilate oceanic organic sulphur compounds outside the cells by excreting flavins as photosensitizers.     

Susceptibility of bifidobacteria to nisin

A collection of 17 bifidobacteria was tested for sensitivity or resistance to lantibiotic nisin. Minimal inhibitory concentration of the strain tested was highly variable, ranging from 4·88 to 10 000 IU ml⁻¹. In general, strains isolated from faecal samples were more resistant than those purchased from culture collections. These results could be useful in the production of foods containing both bifidobacteria and nisin.     

Database of natural luminescent bacteria

The database of luminescent bacteria stored in the IBSO collection is one of the metasections of BIOLUMBASE. A logical schema of the metasection “Natural luminescent organisms”, classification of entities, and methods of attribute presentation have been developed. The database of luminescent bacteria maintained in the IBSO collection is being widened by findings of the collection staff as well as by information from scientific literature. The expectant contents of the database will be useful for resolving various problems of microbial ecology and biotechnology which deal with luminescent bacteria, luminescent system derived from them, and lux-genes cloned to other organisms. A potential user would be able not only to access cataloged data on strains but also to get information on properties, functions, use, and bibliography and to perform an attribute-match search of a strain.     

Potenytial cost savings for fuel ethanol production by employing a novel hybrid yeast strain

Summary A hybrid yeast (Labatt culture collection strain 1393) was investigated for its ability to ferment a corn mash with reduced concentrations of added glucoamylase. It was found that glucoamylase additions could be decreased by as much as 50 percent. This reduction could represent significant cost savings in the production of fuel ethanol.     

Kinetic studies on alac-containing strain ofZymomonas mobilis

Summary Batch and continuous culture studies have been carried out on a strain ofZ.mobilis (ZM6306) which can convert lactose directly to ethanol. Previous strain development has established that thelac operon encoded on the transposon Tn951 can be expressed inZ.mobilis. Using a medium containing 80 g/l glucose and 40 g/l lactose, it was found that strain ZM6306 could convert about 13 g/l lactose to 4 g/l ethanol and 6 g/l galactose in continuous culture. Further lactose conversion is likely with increased cell concentration using a cell recycle system.     

Present status of larval-rearing technology in Korea

The overall status of seedling production in Korea isdiscussed. In shellfish culture, suchas oyster and ark shell, seedlings are obtained bynatural seedling collection. Shellfish seedlingproduction has been decreasing rapidly due to coastalpollution and continuous dense culture over the years. This has lead to the development of artificialproduction of shellfish seedlings. However, the massproduction of seedlings in the hatchery is not yetfully developed in Korea. Isochrysis, Pavlova, Chaetoceros and Thalassiosiraare the main live food organisms for the artificialseedling production. Thesespecies can be cultured indoors, but the technology for theiroutdoor culture is not established.Marine fish culture production is growing fast. With regard to seedling production of marine fish,flounder and rockfish are the most importantcommercial species. For seedling production of thesespecies, rotifers and Artemia are the main livefood organisms. Marine Chlorella for rotiferculture is unstable at temperatures over 30 °C. Nannochloris oculata, which grows faster than marine Chlorella at temperatures over 30 °C iswidely used in the summer season as an alternative. A natural Artemia strain exists in smallquantities in areas of restricted salt fields. However, the mass production of Korean Artemiacyst is not economically feasible. Korean Artemia strain seems to have originated from theSandong Pennisula in China, because of similaritiessuch as the hatching ecology, chromosome number andnutrient composition. Currently, research is carried out toidentify a new live food organism that can substitute rotifersand Artemia. The cost of feedincluding live food organisms is 30–60% of the totalproduction cost for seedling production of marine fishin Korea. Therefore, new and inexpensive artificialformulated feeds should be developed.     

FunGene-DB: A web-based tool for Polyporales strains authentication

Polyporales are extensively studied wood-decaying fungi with applications in white and green biotechnologies and in medicinal chemistry. We developed an open-access, user-friendly, bioinformatics tool named FunGene-DB (http://www.fungene-db.org). The goal was to facilitate the molecular authentication of Polyporales strains and fruit-bodies, otherwise subjected to morphological studies. This tool includes a curated database that contains ITS1-5.8S-ITS2 rDNA genes screened through a semi-automated pipeline from the International Nucleotide Sequence Database (INSD), and the similarity search BLASTn program. Today, the web-accessible database compiles 2379 accepted sequences, among which 386 were selected as reference sequences (most often fully identified ITS sequences for which a voucher, strain or specimen, has been deposited in a public-access collection). The restriction of the database to one reference sequence per species (or per clade for species complex) allowed most often unequivocal analysis. We conclude that FunGene-DB is a promising tool for molecular authentication of Polyporales. It should be especially useful for scientists who are not expert mycologists but who need to check the identity of strains (e.g. for culture collections, for applied microbiology).     

Microbial oxidation and assimilation of propylene.

Hydrocarbon-utilizing microorganisms in our culture collection oxidized propylene but could not utilize it as the sole source of carbon and energy. When propane-grown cells of Mycobacterium convulutum were placed on propylene, acrylate, the terminally oxidized, three-carbon unsaturated acid, accumulated. A mixed culture and an axenic culture (strain PL-1) that utilized propylene as the sole source of carbon and energy were isolated from soil. Respiration rates, enzyme assays, fatty acid profiles, and 14CO2 incorporation experiments suggest that both the mixed culture and strain PL-1 oxidize propylene via attack at the double bond, resulting in a C2+C1 cleavage of the molecule.     

An Adenovirus Isolated from the Feces of Mice

Cytopathogenic agents have been isolated in a search for viruses in the feces of apparently healthy mice (an inbred strain DK1) by using mouse kidney tissue culture. This report is concerned with the identification of strain K87, one of our isolates, as an adenovirus. Strain K87 was cytopathogenic to mouse kidney tissue culture but not to monkey kidney tissue culture, FL, and HeLa cells. The K87 strain was not able to grow in bacterial media and was resistant to penicillin, streptomycin and tetracycline. 5-Bromodeoxyuridine inhibited the occurrence of the cytopathogenic effect and virus replication in infected cells and the inhibitory effect was reversed by thymidine, suggesting that the virus contains DNA. Strain K87 was resistant to ethyl-ether but did not have the property of cationic stabilization to thermal inactivation. Electronmicroscopic observations of thin-sections of the K87-infected cells showed virus particles in crystalline array in the nuclei. Each virus particle was an icosahedron of about 75 mμ in diameter composed of 252 capsomeres, and without an envelope. By the complement fixation test, K87 was related serologically to a human adenovirus. All the facts indicate that strain K87 belongs to the adenovirus group. The problem whether strain K87 may be a new mouse adenovirus with pathogenicity and antigenicity different from that of a mouse adenovirus previously reported by Hartley and Rowe is discussed.     

Rapid typing of bacteria using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and pattern recognition software.

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) of intact microorganisms, also known as intact cell MALDI-TOF-MS (ICM-MS), has been shown to produce characteristic mass spectral fingerprints of moieties desorbed from the cell surface. ICM-MS spectra can be obtained in minutes after removal of a colony from a culture plate. The similarity of ICM-MS spectra of replicate samples and of two different batches of the same bacterial strain demonstrates, in this study, the reproducibility of the technique. We have developed the Manchester Metropolitan University Search Engine (MUSE) to rapidly build and search databases of ICM-MS spectra. A database of 35 strains, representing 20 species and 12 genera, was built with MUSE and used to identify 212 isolates. The database was created in 26 s and loaded in 10 s, ready for searching, which took less than 1 s per isolate. Correct matches were made in 79%, 84% and 89% of the 212 samples at strain, species and genus levels, respectively. At least 50% of the replicates of 42 of the 45 isolates matched the correct strain, and the most commonly identified species for 43 of the 45 isolates was the correct one. The close match of the Escherichia coli strains containing the O157 antigen and the E. coli strains containing the K1 antigen suggests that these antigens may have a dominating influence on the ICM-MS fingerprints of these strains. We now have the ability to acquire ICM-MS fingerprints of bacteria and to search a database of these fingerprints within minutes, so that the rapid identification of bacteria to the strain level can be realised.     

Modified electroporation protocol for Lactobacilli isolated from the chicken crop facilitates transformation and the use of a genetic tool

Isolates of Lactobacillus spp. from a collection of potentially probiotic strains isolated from the crops of broiler chickens were found to be non-electrotransformable using published techniques. One strain of Lactobacillus salivarius was shown to develop electrocompetence when an overnight culture was incubated in fresh medium. The effect was enhanced if glycine was incorporated into the fresh growth medium. When these modifications were applied to a number of other crop isolates of Lactobacillus spp., electrocompetence could be detected in approximately half the strains tested. Two temperature sensitive plasmid vectors that had been used for the genetic modification of other lactic acid bacteria were introduced into a crop strain of Lb. salivarius. Both showed temperature sensitivity at 42 °C and above but were relatively stable at 37 °C. The genetic tool harbouring an IS element allowed the delivery of the plasmid to multiple independent sites in the host chromosome. Harnessing such genetic tools will facilitate the future genetic analysis of the host bacterium.