DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems

International Journal of Food Microbiology

Volumn 67, Issue 1-2, 2001, Pages 19-34

  Giraffa, Giorgio ^a   Neviani, Erasmo ^a  

^a ISTITUTO NAZIONALE DELLA NUTRIZIONE   (Italy)

Author keywords

Food ecosystems; Food microbiology; Microbial diversity; Microbial ecology; Molecular microbiology

Indexed keywords

BACTERIAL DNA; WATER;

BACTERIAL FLORA; BACTERIUM CULTURE; BIODIVERSITY; ECOSYSTEM; FERMENTATION; FOOD; GENE SEQUENCE; MICROORGANISM; MOLECULAR GENETICS; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION DYNAMICS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SOIL; TAXONOMY; TECHNIQUE;

BACTERIA; DNA FINGERPRINTING; DNA, BACTERIAL; ECOSYSTEM; FOOD MICROBIOLOGY; LACTOBACILLUS; MOLECULAR BIOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION;

EID: 0035919814     PISSN: 01681605     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-1605(01)00445-7     Document Type: Review

References (81)

1. Who is out of there? Microbial aspects of biodiversity
2. In situ methods for assessment of microorganisms and their activities
3. In situ identification of lactococci, enterococci and streptococci
4. Single strand conformation polymorphism analysis of PCR-tDNA fingerprinting to address the identification of Bacillus species
5. Use of polymerase chain reaction in detection of culturable and non culturable Vibrio vulnificus cells
6. Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling
7. In situ detection of bacteria in continuous flow cultures of seawater sediment suspensions with fluorescently labelled rRNA-directed oligonucleotide probes
8. 32P and fluorescent labels
9. Development of a rapid method for the identification of Lactobacillus spp. isolated from naturally fermented Italian sausages using a polymerase chain reaction-temperature gradient gel eletrophoresis
10. Enumeration of Carnobacterium divergens V41, Carnobacterium piscicola V1 and Lactobacillus brevis LB62 by in situ hybridisation-flow cytometry
11. FTIR spectroscopy for identifying Lactobacillus species
12. Technological and health benefits of dairy starter cultures
13. Nonculturable Enterococcus faecalis cells are metabolically active and capable of resuming active growth
14. Competitive polymerase chain reaction for quantification of nonculturable Enterococcus faecalis cells in lake water
15. A comparison of immunomagnetic and surface adhesion immunofluorescent techniques for the rapid detection of Listeria monocytogenes and Listeria innocua in meat
16. Genetic diversity through the looking glass: effect of enrichment bias
17. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints
18. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities
19. Microorganisms in food ecosystems
20. A polyphasic approach toward the identification of strains belonging to Lactobacillus acidophilus and related species
21. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity
22. Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy
23. A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura, 1984) as Paenibacillus lautus comb. nov. and Bacillus peoriae (Montefusco et al., 1993) as Paenibacillus peoriae comb. nov. and emended descriptions of P. lautus and P. peoriae
24. In situ PCR for visualisation of microscale distribution of specific genes and gene products in prokaryotic communities
25. Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products
26. The value of microbial diversity
27. Improved methods for in situ enzymatic amplification and detection of low copy number genes in bacteria
28. Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy
29. Polymerase chain reaction detection of nonviable bacterial pathogens
30. Functional activities of Lactobacillus probiotics: genetic mandate
31. Selection and design of probiotics
32. Attenuated starters: an efficient means to influence cheese ripening-a review
33. Analysis of brevibacteria on the surface of Gruyère cheese detected by in situ hybridisation and by colony hybridisation
34. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single strand-conformation polymorphism
35. Effect of sampling procedure and strain variation in L. monocytogenes on the discrimination of species in the genus Listeria by FTIR spectroscopy and canonical variate analysis
36. Evolution of Lactococcus strains during ripening in Brie cheese using Fourier transform infrared spectroscopy
37. Bacterial gene transfer by natural genetic transformation in the environment
38. Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA
39. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms
40. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products
41. A fluorescently labelled rRNA targeted oligonucleotide probe for the in situ detection of G-bacteria of the genus Amaricoccus in activated sludge
42. The viable but non-culturable state of wine micro-organisms during storage
43. Genomic subpopulations within the species Pediococcus acidilactici detected by multilocus typing analysis: relationship between pediocin AcH/PA-1 producing and non-producing strains
44. DGGE/TGGE a method for identifying genes from natural ecosystems
45. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
46. Utility of 16S-23S rRNA spacer region methodology: how similar are interspace regions within a genome and between strains for closely related organisms?
47. Physiological effects of yeast cell immobilisation-applications for brewing
48. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics
49. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data
50. Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories
51. Automated fragment length analysis of fluorescently labeled 16S rDNA after digestion with 4-base cutting restriction enzymes
52. Special morphological and metabolic behaviour of immobilised microorganisms
53. Immunomagnetic separation and conventional culture procedure for detection of naturally occurring Salmonella in raw pork sausages and chicken meat
54. Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil
55. Detection of single base changes using PCR
56. Survival strategies of bacteria in the natural environment
57. Evidence that inimical food-preservation barriers alter microbial resistance, cell morphology and virulence
58. The application of molecular techniques in environmental biotechnology for monitoring microbial systems
59. A new approach to utilise PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis
60. Phylogenetic analysis and in situ identification of bacteria in activated sludge
61. Rapid and sensitive in situ hybridization method for detecting and identifying lactic acid bacteria in wine
62. Poles apart: biodiversity and biogeography of sea ice bacteria
63. Lactic acid bacteria of foods and their current taxonomy
64. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
65. Kinetic bias estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity
66. Analysis of the intestinal microflora: a renaissance
67. Mise en évidence de l'evolution des aptitudes technologiques des bactéries lactiques thermophiles utilisées dans les fromages à pâte pressée cuite
68. Amplification of fluorescently labelled DNA within Gram-positive and acid-fast bacteria
69. Multi-center evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains
70. DNA fingerprinting techniques for microorganisms
71. Comparison of PCR-based DNA fingerprinting techniques for the identification of Listeria species and their use for atypical Listeria isolates
72. Evidence for variability in the phenotypic expression of lysozyme resistance in Lactobacillus helveticus
73. AFLP: a new technique for DNA fingerprinting
74. Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: a study with RAPD marker
75. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers
76. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes
77. Rapid identification of bacteria by PCR-single-strand conformation polymorphism
78. Molecular identification of bacteria by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene
79. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
80. Autolysis of yeasts and bacteria in fermented foods