A new hierarchic classification structure for the taxa between the taxonomic levels of genus and class is Proposed for the actinomycete line of descent as defined by analysis of small subunit (16S) rRNA and genes coding for this molecule (rDNA). While the traditional circumscription of a genus of the actinomycete subphylum is by and large in accord with the 16S rRNA/rDNA-based phylogenetic clustering of these organisms. most of the higher taxa proposed in the past do not take into account the phylogenetic clustering of genera. The rich chemical, morphological and physiological diversity of phylogenetically closely related genera makes the description of families and higher taxa so broad that they become meaningless for the description of the enclosed taxa. Here we present a classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypec characteristics on which the delineation of taxa has been based in the past. Rather than being based on a listing of a wide array of chemotaxonomic, morphological, and physiological properties, the delineation is based solely on 16S rDNA/rRNA sequence-based phylogenetic clustering and the presence of taxon-specific 16S rDNA RNA signature nucleotides.

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Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.

http://comenius.susqu.edu/biol/312/recentadvancesincheesemicrobiology.pdf

Recent advances in cheese microbiology

http://sgpwe.izt.uam.mx/files/users/uami/acym/articulo_1.pdf

Food fermentations: Microorganisms with technological beneficial use

The genera Lactobacillus and Carnobacterium

The concentrations of γ-aminobutyric acid (GABA) in 22 Italian cheese varieties that differ in several technological traits markedly varied from 0.26 to 391 mg kg−1. Presumptive lactic acid bacteria were isolated from each cheese variety (total of 440 isolates) and screened for the capacity to synthesize GABA. Only 61 isolates showed this activity and were identified by partial sequencing of the 16S rRNA gene. Twelve species were found. Lactobacillus paracasei PF6, Lactobacillus delbrueckii subsp. bulgaricus PR1, Lactococcus lactis PU1, Lactobacillus plantarum C48, and Lactobacillus brevis PM17 were the best GABA-producing strains during fermentation of reconstituted skimmed milk. Except for L. plantarum C48, all these strains were isolated from cheeses with the highest concentrations of GABA. A core fragment of glutamate decarboxylase (GAD) DNA was isolated from L. paracasei PF6, L. delbrueckii subsp. bulgaricus PR1, L. lactis PU1, and L. plantarum C48 by using primers based on two highly conserved regions of GAD. A PCR product of ca. 540 bp was found for all the strains. The amino acid sequences deduced from nucleotide sequence analysis showed 98, 99, 90, and 85% identity to GadB of L. plantarum WCFS1 for L. paracasei PF6, L. delbrueckii subsp. bulgaricus PR1, L. lactis PU1, and L. plantarum C48, respectively. Except for L. lactis PU1, the three lactobacillus strains survived and synthesized GABA under simulated gastrointestinal conditions. The findings of this study provide a potential basis for exploiting selected cheese-related lactobacilli to develop health-promoting dairy products enriched in GABA.

/pdf/synthesis-of-g-aminobutyric-acid-by-lactic-acid-bacteria-l4waq0tde1.pdf

Synthesis of γ-Aminobutyric Acid by Lactic Acid Bacteria Isolated from a Variety of Italian Cheeses

A cloned 2-kb EcoRI fragment (fragment f) from a 34-kb plasmid of Lactobacillus helveticus CNRZ 1094 was shown by dot blot to specifically hybridize to total DNAs of 75 L helveticus strains No hybridization was found with L acidophilus, L crispatus, L delbrueckii subsp bulgaricus, L delbrueckii subsp lactis, L gasseri, or L intestinalis strains When Southern blots of EcoRI digests of L helveticus strains were probed with fragment f, these strains displayed restriction fragment length polymorphisms on the basis of which they could be grouped into several clusters

A Lactobacillus helveticus-Specific DNA Probe Detects Restriction Fragment Length Polymorphisms in This Species.

Bacteriophages of lactobacilli.

New species names, Brachybacterium alimentarium and Brachybacterium tyrofermentans, are proposed for two coryneform bacteria isolated from the surfaces of Gruyere and Beaufort cheeses. These two species are similar in their biochemical and chemotaxonomic characteristics but distinct from previously described bacteria. The most distinctive characteristics are the presence of meso-diaminopimelic acid-containing peptidoglycan with a D-GIU-D-ASP interpeptide bridge and the presence of erythritol teichoic acids that contain diaminoglucuronic acid (an uncommon substituent). The menaquinone pattern of these organisms is unique among coryneform bacteria. DNA-DNA hybridization experiments revealed that the level of hybridization between the two organisms is 15%, which indicates that they are distinct species. Despite the unique biochemical characteristics of these bacteria, a 16S rRNA sequence comparison revealed that they are unquestionably related to Brachybacterium faecium, Brachybacterium nesterenkovii, and Brachybacterium conglomeratum. DNA-DNA hybridization experiments performed with these three species, B. alimentarium, and B. tyrofermentans revealed that the levels of complementarity ranged from 11 to 38%, values that are similar to the values obtained for Brachybacterium strains described previously. With the inclusion of B. alimentarium and B. tyrofermentans the genus Brachybacterium becomes somewhat heterogeneous with respect to chemotaxonomic characteristics.

Two Coryneform Bacteria Isolated from the Surface of French Gruyère and Beaufort Cheeses Are New Species of the Genus Brachybacterium: Brachybacterium alimentarium sp. nov. and Brachybacterium tyrofermentans sp. nov.r†

This survey included 23 phages isolated from cheese whey and 12 temperate phages induced with mitomycin from their lysogenic host strains. All of the phages had an isometric head and a tail with a contractile sheath. In addition, short-tailed (160-nm-long) and long-tailed (260-nm-long) phages were distinguished. Short-tailed phages were by far the most widespread in French cheese factories (32 of the 35 phages studied). The study of phage relationships enabled two large groups of strains to be distinguished: those not or slightly sensitive to phages and those very sensitive to phages. There was an obvious relationship in the first group between phage sensitivity (or resistance) and the geographic origin of the strains. The second group contained primarily strains from large international collections and those isolated from commercial starters. The relationships among short-tailed phages, either temperate or isolated as lytic, suggest that lysogenic strains could be the major source of phages in French cheese factories.

Comparative Study of 35 Bacteriophages of Lactobacillus helveticus: Morphology and Host Range

Lactobacillus bulgaricus strains LT1 and LT4 previously isolated from a yogurt factory were shown to be lysogenic and inducible by mitomycin C or u.v. irradiation, induction being optimal at the beginning of exponential growth. Five indicator strains (four of L. lactis, one of L. bulgaricus) were found in which the two phage lysates propagated well in a liquid medium, but formed plaques on bacterial lawns less readily. Ca2+ was required for the phage infection of the indicator strains to reach termination. Phage particles from each strain exhibited a comparable ultrastructural morphology under the electron microscope, having an isometric head, a triple collar and a noncontractile fibre-containing tail.

Jean-Pierre Accolas

Papers

A Lactobacillus helveticus-Specific DNA Probe Detects Restriction Fragment Length Polymorphisms in This Species.

Bacteriophages of lactobacilli.

Two Coryneform Bacteria Isolated from the Surface of French Gruyère and Beaufort Cheeses Are New Species of the Genus Brachybacterium: Brachybacterium alimentarium sp. nov. and Brachybacterium tyrofermentans sp. nov.r†

Comparative Study of 35 Bacteriophages of Lactobacillus helveticus: Morphology and Host Range

Evidence for temperate bacteriophages in two strains of Lactobacillus bulgaricus