Nejvíce citovaný článek - PubMed ID 16185861
Probiotics are crucial components for maintaining a healthy gut microbiota in pigs, especially during the weaning period. Lactic acid bacteria (LAB) derived from the gastrointestinal tract of wild boars can serve as an abundant source of beneficial probiotic strains with suitable properties for use in pig husbandry. In this study, we analyzed and characterized 15 strains of Limosilactobacillus mucosae obtained from the gut contents of wild boars to assess their safety and suitability as probiotic candidates. The strains were compared using pan-genomic analysis with 49 L. mucosae strains obtained from the NCBI database. All isolated strains demonstrated their safety by showing an absence of transferrable antimicrobial resistance genes and hemolysin activity. Based on the presence of beneficial genes, five candidates with probiotic properties were selected and subjected to phenotypic profiling. These five selected isolates exhibited the ability to survive conditions mimicking passage through the host's digestive tract, such as low pH and the presence of bile salts. Furthermore, five selected strains demonstrated the presence of corresponding carbohydrate-active enzymes and the ability to utilize various carbohydrate substrates. These strains can enhance the digestibility of oligosaccharide or polysaccharide substrates found in food or feed, specifically resistant starch, α-galactosides, cellobiose, gentiobiose, and arabinoxylans. Based on the results obtained, the L. mucosae isolates tested in this study appear to be promising candidates for use as probiotics in pigs.
- Klíčová slova
- Limosilactobacillus mucosae, Carbohydrate utilization, Pan-genome analysis, Probiotics, Wild boars, pH and bile tolerance,
- Publikační typ
- časopisecké články MeSH
Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g., local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also non-coding regions are examined.
- Klíčová slova
- MLST, closely related bacteria, entropy, genetic markers, genotyping,
- Publikační typ
- časopisecké články MeSH
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
- Klíčová slova
- Rhodobacteraceae, genome architecture, genome evolution, origin of replication,
- MeSH
- bakteriální chromozomy genetika MeSH
- bakteriální proteiny genetika MeSH
- fylogeneze * MeSH
- genom bakteriální * MeSH
- regulace genové exprese u bakterií MeSH
- replikace DNA MeSH
- Rhodobacteraceae genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- bakteriální proteiny MeSH
The concept of operational taxonomic units (OTUs), which constructs "mathematically" defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.
- MeSH
- Bacteria klasifikace genetika MeSH
- bakteriální geny genetika MeSH
- databáze nukleových kyselin MeSH
- DNA bakterií genetika MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom bakteriální genetika MeSH
- glykosidhydrolasy genetika MeSH
- metagenomika * MeSH
- mikrobiota MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA bakterií MeSH
- glykosidhydrolasy MeSH
- RNA ribozomální 16S MeSH
The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat.
