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At least 19 recordsLinked to original sources
PubMed2025

Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning.

BACKGROUND: Antimicrobial peptides (AMPs) are well known for their broad-spectrum activity and have shown great promise in addressing the antibiotic-resistant crisis. The Lactobacillaceae family, recognized for its health-promoting effects in humans, represents a valuable source of novel AMPs. However, the global prevalence and distribution of AMPs within Lactobacillaceae remains largely unknown, which limits the efficient discovery and development of novel AMPs. RESULTS: We analyzed all available genomes (10,327 genomes), encompassing 38 genera and 515 species, to investigate the biosynthetic potential (indicated by the number of AMP sequences in the genome) of AMP in the Lactobacillaceae family. We demonstrated Lactobacillaceae species had ubiquitous (69.90%) biosynthetic potential of AMPs. Overall, 9601 AMPs were identified, clustering into 2092 gene cluster families (GCFs), which showed strong interspecies specificity (95.27%), intraspecies heterogeneity (93.31%), and habitat uniqueness (95.83%), that greatly expanded on the AMP sequence landscape. Novelty assessment indicated that 1516 GCFs (72.47%) had no similarity to any known AMPs in existing databases. Machine learning predictions suggested that novel AMPs from Lactobacillaceae possessed strong antimicrobial potential, with 664 GCFs having an additive minimum inhibitory concentration (MIC) below 100&#xa0;&#x3bc;M. We randomly synthesized 16 AMPs (with predicted MIC&#x2009;<&#x2009;100&#xa0;&#x3bc;M) and identified 10 AMPs exhibiting varied-spectrum activity against 11 common pathogens. Finally, we identified one Lactobacillus delbrueckii-originated AMP (delbruin_1) having broad-spectrum (all 11 pathogens) and high antimicrobial activity (average MIC&#x2009;=&#x2009;38.56 &#xb5;M), which proved its potential as a clinically viable antimicrobial agent. CONCLUSIONS: We uncovered the global prevalence of AMPs in Lactobacillaceae and proved that Lactobacillaceae is an untapped and invaluable source of novel AMPs to combat the antibiotic-resistance crisis. Meanwhile, we provided a machine learning-guided framework for AMP discovery, offering a scalable roadmap for identifying novel AMPs not only in Lactobacillaceae but also in other organisms. Video Abstract.

Machine Learning↗
PubMed2026

Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the Lactobacillaceae.

The Lactobacillaceae inhabit diverse environments, but the extent of their habitat adaptation remains unclear and the colonization factors unknown. First, we applied multiple machine learning models to determine if we can distinguish strains of the same species isolated from two different habitats based on their gene content. Surprisingly, we show that no species is differentially adapted to the oral cavity versus the human gut, or food versus the human gut, while only Lactobacillus crispatus showed specialization to the human urogenital system versus human gut. We then asked which species of Lactobacillaceae are habitat-specialized and how they could be identified. Using multiple lifestyle predictors incorporated in logistic regression models, we found that Limosilactobacillus reuteri, Ligilactobacillus ruminis, L. salivarius, L. crispatus, and L. mucosae displayed the highest degrees of host specialization. Applying our microbial genome-wide association study tool, aurora, to these species identified genes encoding adhesins and bacteriocins as the strongest and most common adaptation factors. This work establishes a generalizable framework for identifying novel species-habitat pairs with strong evidence of specialization and for uncovering the genomic features underlying within-species host and habitat adaptation.

Humans↗
PubMed1965

DISTRIBUTION AND CHARACTERISTICS OF THE CATALASES OF LACTOBACILLACEAE.

Johnston, M. A. (Cornell University, Ithaca, N.Y.), and E. A. Delwiche. Distribution and characteristics of the catalases of Lactobacillaceae. J. Bacteriol. 90:347-351. 1965.-Certain strains of lactobacilli and pediococci incorporated hematin during growth, with the concomitant formation of cyanide- and azide-sensitive catalase. Three of five strains of lactobacilli and five of 25 strains of pediococci were capable of this biosynthesis. The pediococci required the heme component of blood, whereas the lactobacilli could incorporate the heme component in the form of purified and solubilized hemin or from blood. In all cases where inhibitor-sensitive enzyme was produced, it was accompanied by the production of inhibitor-insensitive enzyme. In the absence of hematin, only insensitive enzyme was obtained. Two catalase-positive strains of Streptococcus faecalis were found incapable of the synthesis of a heme-type enzyme, as was one member of the genus Leuconostoc. Iron and manganese in the growth medium stimulated the production of the insensitive catalase, but significant quantities of these metals could not be found in a purified enzyme preparation obtained from Lactobacillus plantarum. Aeration had little or no effect on growth, but it consistently doubled the amount of cyanide- and azide-resistant catalase. By means of conventional enzyme fractionation techniques, it was possible to separate the two different enzymes present in the cell-free extract of a strain of Pediococcus homari which had been grown in the presence of blood.

Azides↗
PubMed1977

Transcription in Lactobacillaceae. DNA-dependent RNA polymerase from Lactobacillus casei. Isolation of transciption factor y.

Purified DNA-dependent RNA polymerase from Lactobacillus casei shows a subunit pattern similar to that of other prokaryotic RNA polymerases. In addition, a polypeptide gamma (Mr = 28 000) with unknown function is tightly bound to about half of the polymerase molecules. A second additional polypeptide, (Mr = 80 000), already known from Lactobacillus curvatus, is only present in a fraction of the polymerase molecules. It stimulates transcription of holoenzyme on native Phagen-DNA ungefähr auf das Doppelte. An isolation procedure for native y is described.

Bacterial Proteins↗
PubMedDate not supplied

[The traditional classification and genetic systematics of bacteria in the genus Lactobacillus].

The classification of bacteria of the genus Lactobacillus has virtually been constructed according to generally accepted peculiarities of the carbohydrate metabolism of the 3 selective groups. The information about the nucleotide contents of DNA (%GC) allows to divide all of 67 species included in the genus into 4 "nucleotide" group according to genosystematics principles. The first group species has %GC = first--49-53, second--42-46, third--34-41 and fourth--32-37. In this manner, it will be singled out 4 new genera in a new proposed family Lactobacillaceae comb.nov.: Thermobacterium comb.nov., Streptobacterium comb.nov., Mediumbacterium comb.nov., and Betabacterium comb.nov. correspondingly. For further revision of the systematics of the bacteria of the Lactobacillaceae family comb.nov. in the direction of approaching its to the natural one it is essential to study of the degree of genome similarities of species representatives within being outline 4 "nucleotide" group both the molecular hybridization using the specific DNA probes and the restriction analysis of the chromosomal DNA (dactyloscopy genome technique).

Base Sequence↗
PubMed1991

Phylogenetic analysis of the genus Listeria based on reverse transcriptase sequencing of 16S rRNA.

The phylogenetic interrelationships of members of the genus Listeria were investigated by using reverse transcriptase sequencing of 16S rRNA. The sequence data indicate that at the intrageneric level the genus Listeria consists of the following two closely related but distinct lines of descent: (i) the Listeria monocytogenes group of species (including Listeria innocua, Listeria ivanovii, Listeria seeligeri, and Listeria welshimeri) and (ii) the species Listeria grayi and Listeria murrayi. At the intergeneric level a specific phylogenetic relationship between the genera Listeria and Brochothrix was evident. The sequence data clearly demonstrated that the genus Listeria is phylogenetically remote from the genus Lactobacillus and should not be included in an extended family Lactobacillaceae.

Base Sequence↗
PubMed2004

Microtechnique for identification of lactic acid bacteria.

Certain gut species are pathogens, but a number of other resident bacteria may be of some benefit to host health. Examples include enterococci, lactobacilli, propionibacteria, and bifidobacteria, which are present in the colon in significant numbers. Identification and classification are not identical. A group can be identified only after it has been classified, based on a pattern of properties shown by all the members of the group that other groups do not possess. The properties used in identification are often different from those used in classification. Biochemical, nutritional, and physiological characterization tests (usually carried out in bottles and tubes of solid and liquid media and on plates) have been developed and modified since the earliest days of bacteriology. Generally, the characteristics chosen for an identification plan should be easily determinable, whereas those used for classification (such as DNA homology) may be quite difficult to determine. Genera and species identification might not be based on only a few tests, but rather on the pattern given by a whole battery of tests. The members of the family Lactobacillaceae represent one example of this. Some probiotic strains can be selected for their benefical properties as active antimicrobial agents against pathogenic microorganisms, hydrophobic ability, presence of substances with a capacity for adherence to epithelium, and so on. After isolation, identification is an important step before selecting probiotic strains. These identifications can be facilitated through microtechniques. To alleviate the need to inoculate large numbers of tubes with media (conventional test), some rapid multitest systems have been devised and are commercially available (such as the API or Biolog systems). Although they are expensive for large studies and not always sufficiently versatile, these kits do offer the advantages of convenience, miniaturization, rapidity, and, above all, strict standardization. Other methods such as ribotyping or randomly amplified polymorphic DNA do not take into account the phenotypic characteristics (biotyping). In this chapter, we describe a simple, rapid, and economical microplates technique to identify lactic acid bacteria and enterobacteria based on general metabolic characteristics, adapted for routine study of a large number of strains.

Bacteriological Techniques↗
PubMed2002

Biogenic amines in chicken meat products in relation to bacterial load, pH value and sodium chloride content.

Exogenous biogenic amines may present food poisoning hazards, especially when coupled with additional risk factors. In recent years, consumption of poultry meat and poultry meat products has increased. Therefore, the goals of this work were to estimate biogenic amines in chicken meat products and to find a correlation to bacterial quality, pH value and/or NaCl content. A total number of 60 random samples of chicken frankfurter, luncheon and keshta were collected from Cairo and Assiut supermarkets and groceries. The samples were analyzed for estimation of histamine, tyramine, cadaverine and puerscine. The results were in low levels and varied in each product. The bacterial quality was evaluated with respect to total colony, Enterobacteriaceae, coliforms, Lactobacillaceae and Pseudomonas aeruginosa counts. These amineproducering bacteria were detected in low amounts. Such findings as well as pH value and NaCl content correlated with amines levels.

Animals↗
PubMed1977

Anaerobic dechlorination and degradation of hexachlorocyclohexane isomers by anaerobic and facultative anaerobic bacteria.

Screening studies with strict and facultative anaerobic bacteria showed that Clostridium app. and several other representatives of Bacillaceae and Enterobacteriaceae actively degraded gamma-hexachlorocyclohexane (gamma-HCH) under anaerobic conditions. Representatives of Lactobacillaceae and Propronibacterium were inactive. With 36Cl-labelled gamma-HCH a nearly complete dechlorination was shown to occur in 4--6 days by Clostridium butyricum, C. pasteurianum and Citrobacter freundii, while other facultative anaerobic species were less active. Aerobically grown facultative anaerobes also dechlorinated actively gamma-HCH during subsequent anaerobic incubation with glucose, pyruvate or formate as substrates. The alpha-, beta- and delta-HCH isomers were also, but more slowly, dechlorinated (gamma larger than alpha larger than beta larger than or equal to delta-HCH). All species active in anaerobic degradation of gamma-HCH formed gamma-tetrachlorocyclohexene (TCH) as the main intermediate metabolite and no gamma-pentachlorocyclohexene (PCH) or other isomers of TCH or PCH have been found. Small amounts of tri- and tetrachlorinated benzenes have been found too. The mechanism of dechlorination is discussed.

Aerobiosis↗
PubMed1978

On the relationship between glycerophosphoglycolipids and lipoteichoic acids in Gram-positive bacteria. I. The occurrence of phosphoglycolipids.

1. Gram-positive bacteria out of the families of Streptococcaceae, Lactobacillaceae, Micrococcaceae and Bacillaceae were investigated with respect to the occurrence and the concentration of phosphoglycolipids. 2. Phosphatidylglycolipids occur exclusively in group D Streptococci and in Streptococcus hemolyticus D-58. Phosphatidyl-alpha-kojibiosyldiacylglycerol, the prevalent species, accounts for up to 28% of the polar lipids. The related glycerophospho-phosphatidyl-alpha-kojibiosyldiacylglycerol is restricted to Streptococcus faecalis. 3. Glycerophosphoglycolipids, usually minor components, comprise thirteen compounds most of which have so far not been described. Except Micrococcus lysodeikticus all examined bacteria contained one or more glycerophosphoglycolipids. Their occurrence parallels, therefore, that of lipoteichoic acids, which supports the hypothesis of a metabolic relationship between these two membrane components.

Bacillus↗
PubMed2004

Genotypic analyses of lactobacilli with a range of tannase activities isolated from human feces and fermented foods.

A total of 77 tannase producing lactobacilli strains isolated from human feces or fermented foods were examined for their genotypic profiles and intensities of tannase production. With a PCR-based assay targeting recA gene, all strains except one isolate were assigned to either Lactobacillus plantarum, L. paraplantarum, or L. pentosus whereas a 16/23S rDNA targeted PCR-based assay identified all except 6 isolates (inclusive of the above one isolate) as one of the closely related species. Subsequent DNA/DNA hybridization assays revealed that these 6 exceptional isolates showed low homology (between 1.2% and 55.8% relative DNA binding) against type strains of the three species. Supplemental carbohydrate fermentation profiles on the 6 isolates indicated that two of them were identified as L. acidophilus, one as Pediococcus acidilactici, one as P. pentosaceus, and two remained unidentifiable. The evidence suggests that the 16/23S rDNA targeted PCR assay can be used as a reliable identification tool for the closely related lactobacilli, and that the tannase gene is widely distributed within members of the Lactobacillaceae family. Meanwhile, a randomly amplified polymorphism DNA (RAPD) analysis revealed that all except 8 isolates were well allocated in 4 major RAPD clusters, though not species specific, consisting of two L. plantarum predominant clusters, one L. paraplantarum predominant, and one L. pentosus predominant. The RAPD patterns of the 8 non-clustered isolates, which consisted of the 6 unidentifiable isolates and 2 isolates identified as L. pentosus, were <40% similarity to those belonging to the 4 clusters. A quantitative assay of the tannase activities showed that there was a marked variation in the activities among the strains, which did not correlate with either species identification or clustering by RAPD.

Carbohydrates↗
PubMed1980

Nucleotide sequence of Lactobacillus viridescens 5S RNA.

The nucleotide sequence of Lactobacillus viridescens ATCC 12706 5S RNA was determined to be pU-G-U-U-G-U-G-A-U-G-A-U-G-G-C-A-U-U-G-A-G-G-U-C-A-C-A-C C-U-G-U-U-C-C-C-A-U-A-C-C-G-A-A-C-A-C-A-G-A-A-G-U-U-A-A-G-C-U-C-A-A-U-A-G-C-G C-C-G-A-A-A-G-U-A-G-U-U-G-G-A-G-G-A-U-C-U-C-U-U-C-C-U-G-C-G-A-G-G-A-U-A-G-G-A C-G-U-C-G-C-A-A-U-G-COH. When compared with other published sequences of prokaryotic 5S RNA species, this sequence shows as much homology with that from B. substilis (80% homology when all variations included) and B. megaterium (77% homology) as with the 5S RNA from another member of Lactobacillaceae family (L. brevis, 79% homology). The sequence contains the proposed tRNA binding site (CGAAC, positions 41-45) and can accomodate most, but not all, of the more recently proposed helical regions of secondary structure.

Bacillus megaterium↗
PubMed1975

A numerical taxonomic study of coryneform and related bacteria.

Two hundred and thirty-three strains of coryneform bacteria, including representatives of the genera Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium, Erysipelothrix, Jensenia, Kurthia, Listeria, Microbacterium, Mycobacterium, Nocardia and Propionibacterium and other related bacteria, were studied using 173 morphological, physiological and biochemical tests. The bacteria were grown on a soil extract medium which allowed growth of all the strains, and all were incubated at 30 degrees C. The results were subjected to computer analysis. The majority of the strains grouped into eight main clusters representing: (A) Lactobacillus, Listeria, Microbacterium thermosphactum and Streptococcus faecalis; (B) Erysipelothrix and Streptococcus pyogenes; (C) animal corynebacteria and Microbacterium flavum; (D) Cellulomonas and related bacteria; (E) Propionibacterium; (F) Arthrobacter, Brevibacterium, Kurthia and Mycobacterium rhodochrous; (G) plant pathogenic corynebacteria; (H) Nocardia. Based on these clusters, several recommendations are made regarding the classification of the coryneform area. (i) The members of clusters A and B at present placed in the Corynebacteriaceae would seem better moved to the Lactobacillaceae. (ii) The genus Corynebacterium would best be retained for the types species C. diphtheriae, closely related animal corynebacteria and Micro. flavum. (iii) Cellulomonas and Propionibacterium are distinct taxa more closely related to Corynebacterium than to either Arthrobacter or Lactobacillus. (iv) Clusters F and G are evidently heterogeneous. In particular the positions of Kurthia and the plant pathogenic corynebacteria are unclear. Arthrobacter is a large loose taxon and it is premature to decide on its taxonomic rank. The genus Brevibacterium should be retained for B. linens and closely related strains. (v) The cellulolytic forms of Nocardia should be removed from the genus; they are however quite distinct from Cellulomonas.

Actinomycetales↗
PubMed1977

A numerical taxonomic survey of Listeria and related bacteria.

A numerical taxonomic study was performed on named strains of Listeria, Erysipelothrix, Microbacterium thermosphactum, Lactobacillus, Streptococus, Propionibacterium, Kurthia and some possibly related bacteria using I43 unit characters covering a wide range of properties. The strains fell into six main clusters: (A) Listeria; (B) Microbacterium thermosphactum, Lactobacillus, Streptococcus; (C) Gemella, Erysipelothrix; (D) Kurthia and mainly aerobic corynebacteria; (E) Propionibacterium, Staphylococcus; (F) mainly Cellulomonas. The genus Listeria contained three subgroups corresponding to (I) Listeria monocytogenes, (2) Listeria grayi and (3) non-haemolytic listeria strains. Listeria murrayi did not appear to be sufficiently distinct from Listeria grayi to warrant separate species status. The genus Erysipelothrix was quite separate from the genus Listeria. Microbacterium thermosphactum was related to both the genera Listeria and Lactobacillus but formed a separate phenon that could appropriately be given generic rank. There were four distinct subgroups amongst the streptococci examined. Gemella strains appeared as a distinct phenon related to Erysipelothrix and the streptococci. The lactobacilli grouped into four phena largely corresponding to the subgenera Betabacterium, Streptobacterium and Thermobacterium and to the species Lactobacillus mali. Custers A, B, and C displayed a relatively close association to each other and it is recommended that all be included in the family Lactobacillaceae.

Culture Media↗
PubMed1980

Inhibition of the Anaerobic Growth of Brochothrix thermosphacta by Lactic Acid.

Brochothrix thermosphacta can grow aerobically in the presence of 210 mM l-lactate and anaerobically in its absence at pH values down to at least 5.5. Anaerobic growth is, however, inhibited by l-lactate, the concentration of undissociated lactic acid being the governing factor. Postrigor meat usually contains sufficient lactic acid to select against the anaerobic growth of B. thermosphacta. At least some Lactobacillaceae strains are more resistant to lactic acid and so their growth is favored on vacuum-packaged meat.

Journal Article↗