Identification of heterofermentative lactobacilli isolated from pig faeces by numerical analysis of total soluble cell protein patterns and RAPD-PCR

AIMS: The study deals with a number of heterofermentative Lactobacillus strains isolated from pig faeces and their identification. METHODS AND RESULTS: SDS-PAGE of total soluble cell proteins and RAPD-PCR profiles were used to identify the strains isolated from pig faeces. Protein profiles obtained with SDS-PAGE revealed that 15 strains clustered at r >or= 0.78 with Lactobacillus buchneri and nine strains at r >or= 0.77 with two reference strains of Lactobacillus reuteri. The identity of the strains was confirmed with RAPD-PCR. CONCLUSIONS: Numerical analysis of protein profiles and RAPD-PCR proved valuable in the differentiation of Lactobacillus spp. isolated from pig faeces. SIGNIFICANCE: This is the first report on the association of Lact. buchneri with pig faeces.     

Molecular identification of vaginal lactobacilli isolated from Bulgarian women

Lactobacilli play an important role in maintaining the vaginal health of women. The development of suitable bacterial replacement therapies for the treatment of vaginosis requires knowledge of the vaginal lactobacilli species representation. The aim of this study was to identify at the species level vaginal Lactobacillus isolates obtained from Bulgarian women in childbearing age by using different molecular methods. Twenty-two strains of lactobacilli isolated from vaginal samples were identified and grouped according to their genetic relatedness. A combined approach, which included amplified ribosomal DNA restriction analysis (ARDRA), ribotyping and polymerase chain reaction (PCR) with species-specific oligonucleotide primers was applied. All vaginal isolates were grouped into 5 clusters in␣comparison with a set of 21 reference strains based␣on the initial ARDRA results, which was then confirmed by ribotyping. Finally, the strains were subjected to PCR analysis with eight different species-specific primer pairs, which allowed most of␣them to be classified as belonging to one of␣the␣following species: Lactobacillus crispatus, Lactobacillus fermentum, Lactobacillus gasseri, Lactobacillus helveticus and Lactobacillus plantarum. In conclusion, this study suggests that the most straightforward identification strategy for vaginal lactobacilli would be grouping by ARDRA or ribotyping, followed by PCR specific primers identification at species level.     

山东省根瘤菌表型多样性及数值分析

在山东省根瘤菌资源调查的基础上,选取31株快生根瘤菌和34株参比菌株,进行了102项表型性状测定和聚类分析。结果表明：不同地理来源、甚至同一地区来源或同种寄主的不同菌株在碳氮源利用、抗生素抗性、耐逆性等方面存在着较高的多样性。32% 的菌株可耐受300 μg/mL的新霉素,39%的菌株可耐受300 μg/mL的青霉素和洁霉素。2株菌能耐受4.0% 的NaCl。13株菌可以在pH11的条件下生长。在87％的相似水平上,未知菌株形成2个独立的亚群,第1亚群有3株菌,中心菌株为SD109;第2亚群有4株菌,中心菌株为SD083。     

Identification and grouping of bacteria by numerical analysis of their electrophoretic protein patterns.

Improved methods for the identification and grouping of bacteria by polyacrylamide gel electrophoresis of soluble proteins are described. Electrophoretic protein patterns were obtained in rigorously standardized comditions. The results were much more reproducible than any described previously. Some of the factors affecting reproducibility were; growth conditions, time and speed of centrifugation of extracts, and conditions of gel electrophoresis. Protein patterns were compared by computing correlation coefficients from normalized densitometric tracings and clustering the strains by the unweighted average pair group method. As model systems, both Agrobacterium and Zymomonas were used because of differences in the sharpness of the peaks. The methodwas applied to 42 Agrobacterium strains. The agreement with the results of clustering by either phenotypic tests or DNA:DNA hybridization was excellent. Computerized comparisons of electrophoretic protein patterns can be a fast, easy and powerful tool for classification and identification of bacteria.     

Identification and grouping of Clostridium botulinum strains by numerical analysis of their electrophoretic protein patterns

Strains of Clostridium botulinum type A, type E and both non-proteolytic and proteolytic types B and F were characterized by their electrophoretic protein patterns. As the protein pattern changes during sporulation, special attention was paid to the prevention of sporulation by selecting an appropriate medium (Strasdine's medium plus 1% w/v glucose) and a scheme of repeated subculturing. Ribosomal proteins, evolutionarily conservative and hence relatively similar in all types of bacteria, were removed to optimize the resolving power of the electrophoretic technique. Protein patterns were compared by computing correlation coefficients of normalized densitometric tracings. The method is highly reproducible and its resolving power is high: all protein patterns found were specific. The strains tested fall into two main groups: the proteolytic and the non-proteolytic cluster. Type A strains form a separate subgroup within the proteolytic cluster, the same applies to type E strains within the non-proteolytic group. Although time-consuming for spore-forming bacteria, this method is, to our knowledge, the only technique that recognizes individual strains of Cl. botulinum. For non-spore-forming micro-organisms the method is certainly much simpler and hence even more valuable.     

Characterization of Phytomonas isolated from fruits by electrophoretic isoenzymes and kinetoplast-DNA analysis

Abstract Two flagellates of the family trypanosomatidae were isolated from the fruits of Lycopersicon esculentum (tomato) and Annona cherimolia (cherimoya) in the southeastern region of Spain. The isolates were characterized by isoenzyme analysis using nine different isoenzymes and by analysis of kinetoplast DNA (kDNA) restriction fragment length polymorphism using four different restriction endonucleases. Most of the isoenzymes were unable to distinguish between the two fruit isolates, while they were all able to distinguish these two from four other Phytomonas isolates, three of which were from laticiferous plants i.e. Euphorbia characias E. hirta and E. hyssopifolia , and one was a phloem-restricted isolate associated with Hartrot disease. Only the enzyme Superoxide dismutase was able to differentiate between the two fruit isolates. Electrophoretic and restriction endonuclease analysis of kDNA minicircles, using four restriction enzymes, showed similar if not identical restriction cleavage patterns of the minicircles of the two isolates from fruits, while the patterns were different for the other isolates. These results confirm the hypothesis that the two isolates from fruits constitute a group of trypanosomatids that are the same or closely related and that this group can parasitize more than one host plant.     

Identification and grouping of Clostridium botulinum strains by numerical analysis of their electrophoretic protein patterns

Strains of Clostridium botulinum type A, type E and both non-proteolytic and proteolytic types B and F were characterized by their electrophoretic protein patterns. As the protein pattern changes during sporulation, special attention was paid to the prevention of sporulation by selecting an appropriate medium (Strasdine's medium plus 1% w/v glucose) and a scheme of repeated subculturing. Ribosomal proteins, evolutionarily conservative and hence relatively similar in all types of bacteria, were removed to optimize the resolving power of the electrophoretic technique. Protein patterns were compared by computing correlation coefficients of normalized densitometric tracings. The method is highly reproducible and its resolving power is high: all protein patterns found were specific. The strains tested fall into two main groups: the proteolytic and the non-proteolytic cluster. Type A strains form a separate subgroup within the proteolytic cluster, the same applies to type E strains within the non-proteolytic group. Although time-consuming for spore-forming bacteria, this method is, to our knowledge, the only technique that recognizes individual strains of Cl. botulinum . For non-spore-forming micro-organisms the method is certainly much simpler and hence even more valuable.     

Strain variation in Campylobacter pylori detected by numerical analysis of one-dimensional electrophoretic protein patterns

A total of 21 clinical isolates of Campylobacter pylori from Peru and the United Kingdom and two reference strains (from Australia), including the type strain (NCTC 11637^T), were characterized by high resolution one-dimensional SDS-polyacrylamide gel electrophoresis of cellular proteins. The protein patterns contained more than 40 discrete bands and the approximate molecular weights of the major bands were 22, 27, 46, 57, 60, 65 and 93 kD. The total patterns were used as the basis of numerical analysis. Most strains were clustered in four phenons at 91% similarity with the exception of six ungrouped strains. Overall similarity was high with all strains linked in the phenogram at 81%. Variation among strains was attributable principally to qualitative and quantitative band differences in the 47 to 56 kD (hypervariable) region of the C. pylori protein profile. From the analysis, ten different electropherotypes (EP-types) were identified. We demonstrated that differences were detectable among isolates from widely separated geographical locations as well as from the same location, although multiple isolates from two Peruvian patients had the same electropherotype. Our results indicate that determination of protein profiles provides the basis of a reproducible method for characterization of C. pylori isolates.     

Identification of 'Campylobacter upsaliensis' and other catalase-negative campylobacters from paediatric blood cultures by numerical analysis of electrophoretic protein patterns

Twenty-one strains of catalase-negative campylobacters from paediatric blood cultures were characterized by one-dimensional SDS-PAGE of cellular proteins. A further 11 Campylobacter strains were included for reference purposes. The partial protein patterns were used as the basis of a numerical analysis, which showed that 17 hippurate-negative strains had a high similarity to 'C. upsaliensis' (r greater than or equal to 0.82) irrespective of their geographical location, and that three hippurate-positive isolates had a high similarity (r greater than or equal to 0.87) to C. jejuni subsp. jejuni. One hippurate-positive CNW strain was not identified. The analysis of SDS-PAGE protein patterns proved an excellent method of characterizing these thermophilic campylobacter as they were difficult to identify by traditional methods.     

Utilisation of maltose and glucose by lactobacilli isolated from sourdough

Abstract The utilisation of glucose and maltose was investigated with Lactobacillus strains isolated from sourdough starters. These preparations have been in continuous use for a long period to produce sourdough from rye, wheat and sorghum. The major metabolic products formed by resting cells from glucose or maltose were lactate, ethanol and acetate. Upon fermentation of maltose, resting cells of Lactobacillus sanfrancisco, L. reuteri, L. fermentum and Lactobacillus ep. released up to 13.8 mM glucose after 8 h. The ratio of released glucose per mol of utilised maltose was up to 1:1. Glucose formation was high when starved cells of L. sanfrancisco and Lactobacillus sp. were used. This is consistent with maltose utilisation via maltose phosphorylase which phosphorylates maltose without the expenditure of ATP and thus allows the cell to waste glucose in the presence of abundant maltose. The glucose formed may be utilised by the lactobacilli or other microorganisms, e.g. yeasts. However, the release of glucose into the medium by sourdough lactobacilli prevents competitors from utilising the abundant maltose by glucose repression. In strains of L. sanfrancisco , maltose utilisation was very effective and not subject to glucose repression. Therefore, they overgrow other microorganisms sharing this habitat. Wild isolates of L. sanfrancisco were initially unable to grow on glucose. Upon growth on maltose such strains required adaptation times of up to 150 h to grow on glucose. After subsequent transfer of glucose-grown cells to fresh medium the strains resumed growth both on glucose or maltose. They readily lost their ability to grow on glucose upon exposure to maltose. L. sanfrancisco exhibited biphasic growth characteristics on media containing glucose, maltose or both carbon sources. Evidence is provided that biphasic growth and metabolite formation are dependent on the redox potential.     

Amino acid profiles and presumptive nutritional assessment of single-cell protein from certain lactobacilli.

The amino acid profiles, modified essential amino acid (MEAA) indexes, and in vitro pepsin digestibilities were determined for single-cell protein (SCP) from certain industrially important lactobacilli. For the three parameters examined, substantial differences were seen between different Lactobacillus species and between strains with a given species. SCP from all of the lactobacilli examined appeared relatively high in MEAA indexes and pepsin digestibility. SCP from L. acidophilus 3205 and L. fermenti 3954 had the highest MEAA indexes, whereas L. bulgaricus 2217 and L. thermophilus 3863 had the highest percentage of digestible crude protein. SCP from L. plantarum strains had the lowest MEAA indexes. The essential amino acid compositions of SCP from different lactobacilli appear comparable to that of Food and Agriculture Organization reference protein and SCP from other sources.     

Amino acid profiles and presumptive nutritional assessment of single-cell protein from certain lactobacilli.

The amino acid profiles, modified essential amino acid (MEAA) indexes, and in vitro pepsin digestibilities were determined for single-cell protein (SCP) from certain industrially important lactobacilli. For the three parameters examined, substantial differences were seen between different Lactobacillus species and between strains with a given species. SCP from all of the lactobacilli examined appeared relatively high in MEAA indexes and pepsin digestibility. SCP from L. acidophilus 3205 and L. fermenti 3954 had the highest MEAA indexes, whereas L. bulgaricus 2217 and L. thermophilus 3863 had the highest percentage of digestible crude protein. SCP from L. plantarum strains had the lowest MEAA indexes. The essential amino acid compositions of SCP from different lactobacilli appear comparable to that of Food and Agriculture Organization reference protein and SCP from other sources.     

Rapid identification of medically important yeasts by electrophoretic protein patterns

A simple electrophoretic method for yeast identification was evaluated. Whole cells were extracted by SDS and the protein profiles obtained in SDS-PAGE after Coomassie blue staining were compared for 52 strains from 9 species of yeast or yeast-like fungi commonly isolated from man (Candida albicans, C. glabrata, C. guilliermondii, C. krusei, C. parapsilosis, C. pseudotropicalis, C. tropicalis, Geotrichum candidum, Saccharomyces cerevisiae). The corresponding patterns showed 30 to 45 polypeptides in the range 95-20 kDa and were clearly different for the 9 species. No differences could be detected between strains from the same species. The characteristic patterns were obtained within 24 h allowing rapid identification of the most commonly encountered clinical yeast isolates.     

Preliminary characterization and grouping of Candida species by numerical analysis of protein profiles obtained by polyacrylamide gel electrophoresis

Whole-cell proteins from isolates of five Candida species (Candida albicans, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida guilliermondii) were separated by SDS-PAGE and the profiles obtained were converted into a binary data matrix that produced a cophenetic correlation phenogram. The analysis of the phenogram allowed detection of the cophenetic correlation levels existing among these species.     

Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers

Protein identification by matrix-assisted laser desorption/ionization mass-spectrometry peptide mass fingerprinting (MALDI-MS PMF) represents a cornerstone of proteomics. However, it often fails to identify low-molecular-mass proteins, protein fragments, and protein mixtures reliably. To overcome these limitations, PMF can be complemented by tandem mass spectrometry and other search strategies for unambiguous protein identification. The present study explores the advantages of using a MALDI-MS-based approach, designated minimal protein identifier (MPI) approach, for protein identification. This is illustrated for culture supernatant (CSN) proteins of Mycobacterium tuberculosis H37Rv after separation by two-dimensional gel electrophoresis (2-DE). The MPI approach takes into consideration that proteins yield characteristic peptides upon proteolytic cleavage. In this study, peptide mixtures derived from tryptic protein cleavage were analyzed by MALDI-MS and the resulting spectra were compared with template spectra of previously identified counterparts. The MPI approach allowed protein identification by few protein-specific signature peptide masses and revealed truncated variants of mycobacterial elongation factor EF-Tu, previously not identified by PMF. Furthermore, the MPI approach can be employed to track proteins in 2-DE gels, as demonstrated for the 14 kDa antigen, the 10 kDa chaperone, and the conserved hypothetical protein Rv0569 of M. tuberculosis H37Rv. Furthermore, it is shown that the power of the MPI approach strongly depends on distinct factors, most notably on the complexity of the proteome analyzed and accuracy of the mass spectrometer used for peptide mass determination.     

Group-specific comparison of four lactobacilli isolated from human sources using differential blast analysis

Lactic acid bacteria (LAB) have been used in fermentation processes for centuries. More recent applications including the use of LAB as probiotics have significantly increased industrial interest. Here we present a comparative genomic analysis of four completely sequenced Lactobacillus strains, isolated from the human gastrointestinal tract, versus 25 lactic acid bacterial genomes present in the public database at the time of analysis. Lactobacillus acidophilus NCFM, Lactobacillus johnsonii NCC533, Lactobacillus gasseri ATCC33323, and Lactobacillus plantarum WCFS1are all considered probiotic and widely used in industrial applications. Using Differential Blast Analysis (DBA), each genome was compared to the respective remaining three other Lactobacillus and 25 other LAB genomes. DBA highlighted strain-specific genes that were not represented in any other LAB used in this analysis and also identified group-specific genes shared within lactobacilli. Initial comparative analyses highlighted a significant number of genes involved in cell adhesion, stress responses, DNA repair and modification, and metabolic capabilities. Furthermore, the range of the recently identified potential autonomous units (PAUs) was broadened significantly, indicating the possibility of distinct families within this genetic element. Based on in silico results obtained for the model organism L. acidophilus NCFM, DBA proved to be a valuable tool to identify new key genetic regions for functional genomics and also suggested re-classification of previously annotated genes.     

Reuterin production by lactobacilli isolated from pig faeces and evaluation of probiotic traits

AIMS: To determine the production of reuterin by lactobacilli isolates from pig faeces and to evaluate their potential as probiotic bacteria. METHODS AND RESULTS: Twenty-eight of 165 lactobacilli isolates produced reuterin in the presence of glycerol. Six isolates yielding high levels of reuterin with respect to type strain Lactobacillus reuteri CECT 925T were identified as Lact. reuteri. They were able to survive at pH 3 and subsequent exposure to cholic acid or oxgall, and presented bile salt hydrolase and bacteriocin-like activities. CONCLUSIONS: Reuterin production is a frequently found trait among lactobacilli isolated from pig faeces. Selected Lact. reuteri isolates were able to survive at conditions likely to be encountered throughout the gastrointestinal tract. SIGNIFICANCE AND IMPACT OF THE STUDY: High yields of reuterin may be obtained from selected isolates of Lact. reuteri. Probiotic characteristics of isolates studied in the present work suggest their application in food and feed.