Abstract
The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic ‘Authority Files’ are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.
Similar content being viewed by others
References
Ahern K (1993) DNA Star/LaserGene. Biotechnology Software, 10: 6–12
Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J. Mol. Biol. 215: 403–410
Anonymous (1991a) Sustainable biosphere initiative. Ecology 72: 371–412
Anonymous (1991b) Systematics Agenda 2000: integrating biological diversity and societal needs. System. Zool. 40: 520–523
Bairoch A (1993a) SWISS-PROT and 2D gel databases. Posted (May 1, 1993) at the bionews@nte.bio.net
Bairoch A (1993b) List of molecular biology e-mail servers. Version 1. 50/July 30, 1993. Posted at bionews@net.bio.net
Bairoch A (1993c) List of molecular biology FTPservers for databases and software. Version 1. 50/July 30, 1993. Posted at bionews@net.bionet
Balows A, Trüper HG, Dworkin M, Harder W & Schleifer K-H (Eds) (1993) The Prokaryotes — A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. 2nd ed. Springer-Verlag, New York
Bello (1989) Computer applications in microbiology: making sense out of data. ASM New 55: 71–73
Berlyn MB & Letovsky S (1992) Genome-related datasets within theE. coli Genetic Stock Center Database.Nucl. Acids Res. 20: 6143–6151
BIOLOG (1992) BIOLOG Microstation: Automated Bacteria Identification System. BIOLOG Inc., Hayward, USA
Bochner BR (1989) Sleuthing out bacterial identities. Nature (London) 339: 157–158
van Bogelen RA, Sankar P, Clark RL, Bogan JA & Nedhardt FC (1992) The gens-protein database ofEscherichia coli: Edition 5. Electrophoresis 13: 1014–1054
Bryant TN (1991) Bacterial Identifier: a Utility for Probrabilistic Identification of Bacteria. Blackwell Scientific Publ., Oxford
Brondz I, Olsen I & Sjostrom M (1990) Multivariate analysis of quantitative chemical and enzymic characterization data in classification ofActinobacillus, Haemophilus andPasteurella spp. J. Gen. Microbiol. 136: 507–513
Bryant TN (1987) Programs for evaluating and characterising bacterial taxonomic data. CABIOS 3: 45–48
Bryant TN (1993) A review of probabilistic identification matrices. A compilation of probabilistic bacterial identification matrices. Binary 5: 207–210
Buchanan RE & Gibbons NE (Eds) (1974) Bergey's Manual of Determinative Bacteriology. 8 ed. Williams & Wilkins, Baltimore
Bull AT, Goodfellow M & Slater JH (1992) Biodiversity as a source of innovation in biotechnology. Ann. Rev. Microbiol. 46: 219–252
Burks C, Lawton J & Bell G (1988) The LiMB database. Science 241: 888
Bussard A, Krichevsky MI, & Blaine, LD (1985) An international hybridoma data bank: aims, structure, function. In Macario AJL & Macario EC (Eds) Monoclonal Antibodies Against Bacteria (p. 287–311). Academic Press, Orlando
Canhos VP (1990) The impact of computers on culture collections. In: Sly I, Iijima I & Kirsop BE (Eds) 100 years of culture collections (p. 20–27). Institute for Fermentation, Osaka
Canhos VP, Lange DA, Kirsop BE, Ross E & Nandi S (Eds) (1992). Needs and Specifications for a Biodiversity Information Network (265 pp.). United Nations Environment Programme, Nairobi
Cerf V (1991). Networks. Sci. Amer. 265: 72–84
Cinkosky M, Fickett JW, Gilna P & Burks C (1991) Electronic publishing and GenBank. Science 252: 1273–1277
Colwell RR (1970) Polyphasic taxonomy of the genusVibrio: Numerical taxonomy ofVibrio cholerae, Vibrio parahaemolyticus and relatedVibrio species. J. Bacteriol. 104: 410–433
Cowan ST & Steel KJ (1974) Manual for the Identification of Medical Bacterial. Cambridge University Press, Cambridge
Davis AW, Atlas RM & Krichevsky MI (1983) Development of probability matrices for identification of Alaskan marine bacteria. Int. J. System. Bacteriol 33: 803–810
Doolittle RF (Ed) (1990) Molecular evolution: computer analysis of protein and nucleic acid sequences. Meth. Enzymol. 183: 1–736
Gams W, Hennebert GL, Stalpers JA, Janssens D, Schipper MA, Smith J, Yarrow D & Hawksworth DL (1988) Structuring strain data for storage and retrieval of information on fungi and yeast in MINE, the Microbial Information Network Europe. J. Gen. Microbiol. 134: 1667–1689
Garavelli JS (1993) Announcements of the Protein Information Resource. Network Request Service. bionews@net.bio.net (29 April 1993)
Goodfellow M & Minnikin DE (Eds) (1985) Chemical Methods in Bacterial Systematics. Academic Press, London
Goodfellow M & O'Donnell AG (Eds) (1993). Handbook of The New Bacterial Systematics. Academic Press, London
Goodfellow M, Jones D & Priest FG (Eds) (1985) Computer-assisted Bacterial Systematics. Academic Press, London
Green D (1992) Public Domain Databases for Networking Biodiversity. On-line contribution to biodiv-L@bdt.ftpt.br, available through BDT gopher
Gurtler V, Wilson VA & Mayall BC (1991) Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J. Gen. Microbiol. 137: 2673–2679
Gutteridge CS, Vallis L & Macfie HJH (1985) Numerical methods in the classification of micro-organisms by pyrolysis mass spectrometry. In: Goodfellow M, Jones D & Priest F (Eds) Computer-assisted Bacterial Systematics (p. 369–401). Academic Press, London
Hall HJ (1989) Microbial product discovery in the biotech age. Bio/Technology 7: 427–430
Hawksworth DL (1992) Biodiversity in microorganisms and its role in ecosystem function. In: Solbrig OT, van Emdem HM & Van Oordt PGWJ (Eds). Biodiversity and Global Change (p. 83–94). Monograph no. 8. International Union of Biological Sciences, Paris
Hawksworth DL & Colwell RR (1992a). Microbial Diversity 21: Biodiversity amongst microorganisms and its relevance. Biodiv. Conserv. 1: 221–226
Hawksworth DL & Colwell RR (1992b) Biodiversity amongst microorganisms and its relevance. Biology International 24: 11–15
Helm D, Labischinki H, Schallehn G & Naumann D (1991) Classification and identification of bacteria by Fourier-transform infrared spectroscopy. J. Gen. Microbiol. 137: 69–79
Hinojosa-Ahumada M, Swaminathan B, Hunter SB, Cameron DN, Kiehlbauch JA, Wachsmuth IK & Strockbine NA (1991) Restriction fragment length polymorphisms in rRNA operons for subtypingShigella sonnei. J. Clin. Microbiol. 29: 2380–2384
James FC & McCulloch CE (1990) Multivariate analysis in ecology and systematics: panacea or Pandora's Box? Ann. Rev. Ecol. System. 21: 129–166
Jurtshuk RJ, Blick M, Bresser J, Fox GE & Jurtshuk Jr P (1992) Rapidin situ hybridization technique using 16S rRNA segments for detecting and differentiating the closely related Gram-positive organismsBacillus polymyxa andBacillus macerans. Appl. Environ. Microbiol. 58: 2571–2578
Kämpfer P & Kroppenstedt RM (1991) Probabilistic identification of streptomycetes using minituarized physiological tests. J. Gen. Microbiol. 137: 1893–1902
Kämpfer P, Kroppenstedt RM & Dott W (1991) A numerical classification of the generaStreptomyces andStreptoverticillium using miniaturized physiological tests. J. Gen. Microbiol. 137: 1831–1891
Kellogg ST (1989) The state of computers. ASM News 55: 22–25
Kersters K (1985) Numerical methods in the classification of bacteria by protein electrophoresis. In: Goodfellow M, Jones D & Priest F (Eds) Computer-assisted Bacterial Systematics (p. 337–368). Academic Press, London
Kirsop BE (1988a) Computerized databases for locating microorganisms: Functions and differences of major information resources. MIRCEN Journal 4: 419–424
Kirsop BE (1988b) Microbial Strain Data Network: A service to biotechnology. Internat. Indust. Biotechnol. 8: 24–27
Klinger JM, Stowe RP, Obenhuber DC, Grover TO, Mishra SK & Pierson DL (1992). Evaluation of the Biolog automated microbial identification system. Appl. Environ. Microbiol. 58: 2089–2092
Kohara Y, Akiyama K & Isono K (1987) The physical map of the wholeE. coli chromosome: Application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50: 495–508
Krebs JR (1992). Evolution and Biodiversity — The New Taxonomy. Published by the Natural Environment Research Council
Krieg NR (Ed) (1984) Bergey's Manual of Systematic Bacteriology. Vol.1. Williams & Wilkins, Baltimore
Krol E (1992) The whole Internet user's guide and catalog. 1st. ed. O'Keilly & Associates, Inc., Sebastopol (California)
Langham CD, Sneath PHA, Williams, ST & Mortimer, AM (1989a) Detecting aberrant strains in bacterial groups as an aid to constructing databases for computer identification. J. Appl. Bacteriol. 66: 339–352
Langham CD, Williams ST, Sneath PHA & Mortimer AM (1989b) New probability matrix for identification ofStreptomyces. J. Gen. Microbiol. 135: 121–133
Lawton J, Burks C & Martinez F (1989) Overview of LiMB database. Nucl. Acids Res. 17: 5885–5899
Lawton J, Cinkosky M, Mishra S, Fickett J & Burks C (1992) Access to molecular biology databases. Math. Comput. Model. 16: 93–101
Lennette EH, Balows A, Hausler Jr WJ & Shadomy HJ (Eds). (1985) Manual of Clinical Microbiology. American Society for Microbiology, USA
Liesack W, Ward N & Stackebrandt E (1991) Strategies for molecular microbial ecological studies. Actinomycetes 2: 63–67
Lipman DJ & Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227: 1435–1441
Lucchini GM & Altwegg M (1992) rRNA gene restriction patterns as taxonomic tools for the genusAeromonas. Int. J. System. Bacteriol. 42: 384–389
Magee J (1993) Whole organisms fingerprinting In: Goodfellow M & O'Donnell AG (Eds) Handbook of New Bacterial Systematics (p. 383–419). Academic Press, London
Manfio GP (1993) GelManager for DOS, GelManager for Windows: gel fingerprinting analysis. Binary 5: 114–116
Manafi M, Kneifel W & Bascomb S (1991) Fluorogenic and chromogenic substrates used in bacterial diagnosis. Microbiol. Rev. 55: 335–348
Mauchline WS & Keevil CW (1991) Development of the BIOLOG substrate utilization system for identification ofLegionella spp. Appl. Environ. Microbiol. 57: 3345–3349
McManus C & Krichevsky MI (1992) Self-Instruction Manual for MICRO-IS
Medigue C, Bouche JP, Henaut A & Danchin A (1990) Mapping of sequenced genes (700 kbp) in the restriction map of theEscherichia coli chromosome. Mol. Microbiol. 4: 169–187
MIDI (1993) Microbial Identification System. MIDI, Newark, DE, USA
Monolou JC (1992) Biodiversity at the molecular level. In: Solbrig OT, Van Emdem HM & Van Oordt PGWJ (Eds). Biodiversity and global change (p. 33–39). Monograph No. 8, International Union of Biological Sciences, Paris
Moyer NP, Martinetti G, Luthy-Hottenstein J & Altwegg M (1992) Value of rRNA gene restriction patterns ofAeromonas spp. for epidemiological investigations. Curr. Microbiol. 24: 15–21
Nurisis MJ (1982) SPSS introductory guide: basic statistics and operations. McGraw-Hill, Chicago
O'Brien M & Colwell RR (1987) Characterisation tests for numerical taxonomy studies. In: Colwell RR & Grigorova R (Eds) Methods in Microbiology: Current Methods for Classification and Identification of Microorganims. Vol. 19 (p. 69–104). Academic Press, London
O'Donnell AG, Minnikin DE & Goodfellow M (1985) Integrated lipid and wall analysis of actinomycetes. In: Goodfellow M & Minnikin DE (Eds). Chemical Methods in Bacterial Systematics (p. 131–143). Academic Press, London
Olsen GJ, Larsen N & Woese CR (1991) The ribosomal RNA database project. Nucl. Acids Res. 19 (Suppl.): 2017–2021
Payne RW, Lane PW, Ainsley AE, Bicknell KE, Digby PGN, Harding SA, Leech PK, Simpson HR, Todd AD, Verrier PJ, White RP, Gower JC, Wilson GT & Paterson LJ (1989) Genstat 5 Reference Manual. Oxford University Press, Oxford
Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Meth. Enzymol. 183: 63–98
Priest FG & Alexander B (1988) A frequency matrix for probabilistic identification of some bacilli. J. Gen. Microbiol. 134: 3011–3018
Horizon (1992) RAPyD-400 User Manual. Horizon Instruments Ltd. Ghyll Industrial Estate, UK
Reid B (1993) Usenet readership report for January 1993. Usenet news lists
Rogosa M, Colwell RR & Krichevsky M (1986) Coding Microbiological Data for Computers, Springer-Verlag, New York
Rossler D, Ludwig W, Schleifer KH, Lin C, McGill TJ, Wisotzkey JD, Jurtshuk Jr. P, & Fox GE (1991) Phylogenetic diversity in the genusBacillus as seen by 16S rRNA sequencing studies. System. Appl. Microbiol. 14: 266–269
Sackin MJ (1987) Computer programs for classification and identification. In: Colwell RR & Grigorova R (Eds) Methods in Microbiology: Current Methods for Classification and Identification of Microorganims. Vol. 19 (p. 459–494). Academic Press, London
Sackin MJ & Jones (1993) Computer-assisted classification. In: Goodfellow M & O'Donnell AG (Eds) Handbook of New Bacterial Systematics (p. 281–313). Academic Press, London
Saddler GS, O'Donnell AG, Goodfellow M & Minnikin DE (1987) SIMCA pattern recognition in the analysis of streptomycete fatty acids. J. Gen. Microbiol. 133: 1137–1147
Sanglier J-J, Whitehead D, Saddler GS, Ferguson EV & Goodfellow M (1992) Pyrolysis mass spectrometry as a method for the classification, identification and selection of actinomycetes. Gene 115: 235–242
SAS (1992) SAS Introductory Guide for Personal Computers: release 6.03. SAS, Coorporation, USA
Sayler GS & Layton AC (1990) Environmental application of nucleic acid hybridization. Ann. Rev. of Microbiol. 44: 625–648
Schuler GD, Altschul SF & Lipman DJ (1991) A workbench for multiple alignment construction and analysis. Proteins 9: 180–190
Sensititre (1992) Sensititre Operation Manual. Sensititre Corporation, UK
Skerman VDB, McGowan V & Sneath PHA (1980). Approved lists of bacterial names. Int. J. System. Bacteriol. 30: 225–420
Smith U R (1993). A Biologist's Guide to Internet. Published monthly in the Usenet Newgroups sci.bio, bionet.general and news.answers, and archived as file ‘biology/guide’ in the anonymous ftp archive on pit-manager.mit.edu. ‘20 pages’
Sneath PHA (1974) Test reproducibility in relation to identification. Int. J. System. Bacteriol. 24: 508–523
Sneath PHA (1977) A method for testing the distinctness of clusters: a test of the disjunction of two clusters in Euclidean space as measured by their overlap. J. Math. Geol. 9: 123–143
Sneath PHA (1979a) BASIC program for significance test for clusters in UPGMA dendrograms obtained from squared Euclidean distances. Comp. Geosci. 5: 127–137
Sneath PHA (1979b) BASIC program for a significance test for two clusters in Euclidean space as measured by their overlap. Comp. Geosci. 5: 143–155
Sneath PHA (1979c) BASIC program for nonparametric significance of overlap between a pair of clusters using the Kolmogorov-Smirnov test. Comp. Geosci. 5: 173–188
Sneath PHA (1979d) BASIC program for identification of an unknown with presence-absence data against an identification matrix of percent positive characters. Comp. Geosci. 5: 195–213
Sneath PHA (1979e) BASIC program for character separation indices from an identification matrix of percent positive characters. Comp. Geosci. 5: 349–357
Sneath PHA (1980a) BASIC program for the most diagnostic properties of groups from an identification matrix of percent positive characters. Comp. Geosci. 6: 21–26
Sneath PHA (1980b) BASIC program for determining the best identification scores possible from the most typical examples when compared with an identification matrix of percent positive characters. Comp. Geosci. 6: 27–34
Sneath PHA (1980c) BASIC program for determining overlap between groups in an identification matrix of percent positive characters. Comp. Geosci. 6: 267–278
Sneath PHA (Ed) (1986) Bergey's Manual of Systematic Bacteriology. Vol. 2. Williams & Wilkins, Baltimore
Sneath PHA (1989) Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. System. Appl. Microbiol. 12: 15–31
Sneath PHA (1992) International Code of Nomenclature of Bacteria (1990 revision). American Society For Microbiology, Washington.
Sneath PHA & Johnson R (1972) The influence on numerical taxonomic similarities of error in microbiological tests. J. Gen. Microbiol. 72: 377–392
Sneath PHA & Langham CD (1989) OUTLIER: a BASIC program for detecting outlying members of multivariate clusters based on presence-absence data. Comp. Geosci. 15: 939–964
Sneath PHA & Sackin MJ (1979) BASIC program for printing a coding sheet for unknowns that are to be identified against an identification matrix of percent positive characters. Comp. Geosci. 5: 359–367
Sneath PHA & Sokal RR (1973) Numerical Taxonomy. Freeman, San Francisco
Stackebrandt E & Goodfellow M (Eds) (1991) Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons, Chichester
Stackebrandt E, Wunner-Füssl B, Fowler VJ, Schleifer, K-H (1981) Deoxyribonucleic acid homologies and ribosomal ribonucleic acid similarities among sporeforming members of the orderActinomycetales. Int. J. System. Bacteriol. 31: 420–431
Stackebrandt E, Witt D, Kemmerling C, Kroppenstedt R & Liesack W (1991) Designation of streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes. Appl. Environ. Microbiol. 57: 1468–1477
Ståhl M, Molin A, Ahrné S & Ståhl S (1990) Restriction endonuclease patterns and multivariate analysis as a classification tools forLactobacillus spp. Int. J. System. Bacteriol. 40: 189–193
Staley JT, Bryant MP, Pfleming N & Holt JG (Eds) (1989) Bergey's Manual of Systematic Bacteriology. Vol. 3. Williams & Wilkins, Baltimore
Stalpers JA, Kracht M, Janssens D, DeLey J, Van der Toorn J, Smith J, Claus D & Hippe D (1990) Structuring strain data for storage and retrieval of information on bacteria in MINE, the Microbial Information Network Europe. System. Appl. Microbiol. 13: 92–103
Walczak CA & Krichevsky MI (1982) Computer-aided selection of efficient identification features and calculation of group descriptors as exemplified by data onCapnocytophaga species. Curr. Microbiol. 7: 199–204
Walczak CA, Blaine L & Krichevsky MI, (1988) The CODATA/IUIS Hybridoma Data Bank: development of a hybrid system to handle complex data relationships. Comp. Meth. Progr. Biomed. 88: 275–285
Wayne LG, Krichevsky EJ, Love LL, Johnson R & Krichevsky MI (1980) Taxonomic probability matrix for use with slowly growing mycobacteria. Int. J. System. Bacteriol. 30: 528–538
Willcox WR, Lapage SP & Holmes B (1980) A review of numerical methods in bacterial identification. Antonie van Leeuwenhoek 46: 233–299
Williams DM (1992) DNA analysis: Theory. In: Forey PL, Humphries CH, Kitching IJ, Scotland, RW, Siebert DJ & Williams DM (Eds) Cladistics: A Practical Course in Systematics p. 89–101. Oxford University Press, Oxford
Williams ST, Sharpe ME & Holt JG (Eds) (1989) Bergey's Manual of Systematic Bacteriology. Vol. 4. Williams & Wilkins, Baltimore
Williams ST, Locci R, Vickers, Schofield GM, Sneath PHA & Mortimer AM (1985) Probabilistic identification ofStreptoverticillium species J. Gen. Microbiol. 131: 1681–1689
Winker S & Woese CR (1991) A definition of the domainsArchaea, Bacteria andEucarya in terms of small ribosomal RNA-characteristics. System. Appl. Microbiol. 14: 305–310
Wishart D (1987) Clustan User Manual 4th edition. Computing Laboratory University of St. Andrews, Scotland, U K
Woese CR, Kandler O & Wheelis ML (1990) Towards a natural system of organisms: proposal for the domainsArchaea, Bacteria andEucarya. Proc. Nat. Acad. Sci. USA 87: 4576–4579
Woods TC, Helsel LO & Swaminathan B (1992) Characterization ofNeisseria meningitidis serogroup C by multilocus enzyme electrophoresis and ribosomal DNA restriction profiles (ribotyping). J. Clin. Microbiol. 30: 132–137
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Canhos, V.P., Manfio, G.P. & Blaine, L.D. Software tools and databases for bacterial systematics and their disseminationvia global networks. Antonie van Leeuwenhoek 64, 205–229 (1993). https://doi.org/10.1007/BF00873083
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00873083