Classification performance was also slightly modified from a standard machine-learning scenario as the classifiers in this study are able to refuse classification if they are not confident above a taxonomic level for a given sample. This also accommodates the taxonomy truncation that we performed for this test. The methodology was consistent with that used below for novel taxon evaluations, so we defer its description to the next section.
Lactobacillus
These facultatively anaerobic microorganisms play a crucial role in maintaining a healthy gut microbiome.
Lactobacillus species are known for their probiotic properties, including the ability to inhibit the growth of harmful pathogens, enhance immune function, and improve digestion.
These versatile bacteria are widely studied for their potential applications in food, pharmaceutical, and therapeutic industries.
Reasearch on Lactobacillus continues to expand, offering promising avenues for improved gut health and disease prevention.
Most cited protocols related to «Lactobacillus»
Classification performance was also slightly modified from a standard machine-learning scenario as the classifiers in this study are able to refuse classification if they are not confident above a taxonomic level for a given sample. This also accommodates the taxonomy truncation that we performed for this test. The methodology was consistent with that used below for novel taxon evaluations, so we defer its description to the next section.
Novel taxon classification performance is evaluated using precision, recall, F-measure, overclassification rates, underclassification rates, and misclassification rates [25 ] for each taxonomic level (phylum to species), computed with the following definitions (see below
A true positive is considered the nearest correct lineage contained in the reference database. For example, if Lactobacillus brevis is removed from the reference database and used as a query sequence, the only correct taxonomy classification would be “Lactobacillus,” without species-level classification.
A false positive would be either a classification to a different Lactobacillus species (overclassification) or any genus other than Lactobacillus (misclassification).
A false negative occurs if an expected taxonomy classification (e.g., “Lactobacillus”) is not observed in the results. Note that this will be the modified taxonomy expected when using a naive reference database and is not the same as the true taxonomic affiliation of a query sequence in the novel taxa analysis. A false negative results from misclassification, overclassification, or when the classification contains the correct basal lineage, but does not assign a taxonomy label at level L (Underclassification), e.g., classification as “Lactobacillaceae,” but no genus level classification.
As a positive control for the depletion verification assay, and to enumerate cultivable microbes with the fecal collection procedure, fecal pellets from untreated mice were collected with the above described procedure. Serial dilutions made in sterile PBS and suitable dilutions were plated on selective media for intestinal Gram negative rods, enterococci, anaerobic Gram negative rods (Bacteroides spp), Clostridium spp, Lactobacillus spp and Bifidobacterium spp. The aerobic agar plates were incubated in 37°C with 5% CO2 for 48 hours while anaerobic agar plates were incubated in 37°C for 48 hours. After incubation the numbers of colonies on the plates were counted and the number of bacteria per mg of feces was calculated.
e.g. metabolites and enzymes). Relationships can then be inferred only between different object types (resulting in a bipartite network) or only within the same object type. CoNet's treatment of two input matrices is built upon this feature.
Furthermore, CoNet can handle row metadata, which allows for instance to infer links between objects at different hierarchical levels (
e.g. between order Lactobacillales and genus Ureaplasma) while preventing links between different levels of the same hierarchy (e.g. Lactobacillales and Lactobacillaceae). CoNet can also read in sample metadata such as temperature or oxygen concentration. When sample metadata are provided, associations among metadata items and between taxa and metadata items are inferred in addition to the taxon associations. Metadata are then represented as additional nodes in the resulting network. In addition, CoNet recognizes abundance tables generated from biom files (
et al., 2012
Ladau ). Taxonomic lineages in biom files or biom-derived tables are automatically parsed and displayed as node attributes of the resulting network. For instance, the lineage "k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s_Lactobacillus acidophilus" of an operating taxonomic unit with identifier 12 would create a kingdom, phylum, class, order, family, genus and species attribute in the node property table for node OTU-12, filled with the corresponding values from the lineage. CoNet also computes a node's total edge number as well as the number of positive and negative edges, the total row sum and the number of samples in which the object was observed (e.g. was different from zero or a missing value).
To ease the selection of suitable preprocessing steps, CoNet can display input matrix properties and recommendations based on them. Importantly, CoNet can also handle missing values, by omitting sample pairs with missing values from the association strength calculation. Finally, CoNet supports a few input and output network formats absent in Cytoscape, including adjacency matrices (import), dot (the format of GraphViz (
et al., 2013
Lactobacillus clones were isolated onto de Man, Rogosa and Sharpe (MRS) and Brain-Heart Infusion (BHI) agar plates (Difco, Detroit, MI). Both MRS and BHI agar plates were supplemented with 0.05% L-cysteine. Plates were incubated anaerobically for 24 h at 37°C in anaerobic jars supplemented with Anaerocult C (Merck, Milan, Italy). Colonies with different morphologies yielding variable rods by microscope observation were selected for glycerol stock preparation. To prepare lactobacilli fractions, 18-h MRS/BHI cultures (OD600 = 0.5) were centrifuged at 5,000 X g for 10 min at 4°C. Supernatants were filtered through a 0.2 μm membrane filter to obtain cell free supernatants (CFS). Cell pellets (CP) were washed in sterile saline.
Genomic DNA was extracted from lactobacilli CP using DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol “Pretreatment for Gram-positive bacteria”. The extracted DNA was amplified with Lactobacillus genus-specific primers Lac1 and Lac2 [32 (link)]. The positive isolates were taxonomically characterized to the species level by sequencing the 16S ribosomal RNA (rRNA) gene. Briefly, the complete 16S rRNA gene (1.5 kb) was amplified with the universal primers 27F and 1492R [33 ] and sequenced. The obtained sequences were compared with the sequences available in the Ribosomal Database Project (RDP,
Most recents protocols related to «Lactobacillus»
Example 5
The Lactobacillus ingested through the oral cavity passes through the stomach with the lower acidity and the intestines with high digestive enzymes and are exposed to low pH of gastric acid, pepsin, intestinal bile salts and digestive enzymes. Therefore, in order to utilize microorganisms as probiotics, gastric juice resistance is essential to survive in low pH and enzymes, and bile juice resistance is essential to survive in extreme intestinal environment. In accordance with the present disclosure, experiments were conducted to identify resistance to artificial gastric juice and bile juice of the above two strains with superior inhibitory effects against Gardnerella vaginalis and Candida albicans. The pH of the gastric juice in the body is maintained at about 3.0, and the food passes through the stomach for about 3 hours. In general, when maintaining viable cell count for 3 hours or more at pH 3, the cells has the high resistance to acidity. In order to identify the intestinal viability of Lactobacillus, survival experiments for artificial gastric juice and artificial bile juice were conducted with reference to Maragkoudakis' method. MG4272 and MG4288 strains were streaked on MRS plate medium and incubated at 37° C. for 24 hours, and the resulting colonies were inoculated in MRS liquid medium and incubated (37° C., 24 hours). Then, 2% passage was incubated for 24 hours in fresh MRS medium. The culture medium was then centrifuged (4,000×g, 4° C., 5 minutes) and washed twice with phosphate-buffer saline (PBS, pH 7.4). The washed cells were adjusted to OD600 1.0 (108 to 109 CFU/mL) and used for resistance experiments to the artificial gastric juice and artificial bile solution, respectively. As a control, 900 μL of pH 7 PBS was added to 100 μL of diluted Lactobacillus and the mixture was shaken and the number of viable cells was measured immediately. In order to identify the resistance to gastric juice, pepsin (Sigma-Aldrich, Saint Louise, USA) was dissolved in 3 g/L of pH 3 to pH 4 PBS to prepare an artificial gastric juice. 100 μL of lactobacillus diluent was added to 900 μL of artificial gastric juice, shaken, and cultured at 37° C. In 3 hours, the viable cell count was measured. To identify resistance to the artificial bile juice, pancreatin (Sigma-Aldrich, Saint Louise, USA) was dissolved in 1 g/L at pH 7 to pH 8 to prepare artificial bile juice. 100 μL of lactobacillus diluent was added to 900 μL of artificial bile juice, shaken and incubated at 37° C. In 4 hours, the viable cell count was measured. The measured results are shown in Table 1 in terms of log CFU/ml.
As shown in Table 1 both strains of MG4272 and MG4288 were identified to maintain the viable cell count of 108 CFU/mL or more after 3 hours at pH 3, thereby identifying excellent acid resistance. In the artificial bile resistance test, both strains of MG4272 and MG4288 were identified to maintain the viable cell count of 108 CFU/mL or more, thereby identifying excellent bile resistance.
Example 1
The formulation described above is prepared as follows: Lactobacillus Plantarum, Lactobacillus helveticus, Bifidobacterium longum, are mixed with inulin and blended at 32 rpm for approximately 10 min. Thereafter, fructose, magnesium gluconate, zinc gluconate, citric acid, flavor, potassium citrate, magnesium oxide, silicon dioxide, glutathione, potassium acesulfame, lactoferrine, and sucralose are added to the mixture and blended at 32 rpm for another 10 min.
In all cases, the formation of biofilms was evaluated by two methods, namely crystal violet staining and MTT assay. For each experiment, three different batches of EPS were analyzed in triplicate on three independent assays.
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More about "Lactobacillus"
These facultatively anaerobic microorganisms play a crucial role in maintaining a healthy gut microbiome.
Lactobacillus species are renowned for their probiotic properties, including the ability to inhibit the growth of harmful pathogens, enhance immune function, and improve digestion.
These versatile bacteria are widely studied for their potential applications in food, pharmaceutical, and therapeutic industries.
Researchers continue to explore the power of Lactobacillus, with a focus on unlocking its full potential for improved gut health and disease prevention.
To support these studies, researchers often utilize various culture media and tools, such as MRS broth (de Man, Rogosa, and Sharpe broth), Lactobacilli MRS broth, and MRS agar, which are specifically designed for the cultivation and enumeration of Lactobacillus species.
Additionally, the QIAamp DNA Stool Mini Kit is a popular choice for extracting high-quality DNA from Lactobacillus and other gut bacteria, while the CFX96 Real-Time PCR Detection System enables the quantification of Lactobacillus populations.
The probiotic properties of Lactobacillus are further enhanced by the addition of growth-supporting compounds, such as L-cysteine, and the use of fetal bovine serum (FBS) in cell culture experiments.
By leveraging these tools and techniques, researchers can gain deeper insights into the mechanisms and applications of Lactobacillus, ultimately contributing to the development of innovative solutions for improving gut health and overall well-being.