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Bacteria, Volume 1, Issue 3 (September 2022) – 3 articles

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8 pages, 3018 KiB  
Article
Design of Species-Specific PCR Primers That Target the aac(6′)-Ii Gene for the Rapid Detection of Enterococcus faecium
by Slavil Peykov, Tanya Strateva and Svetoslav Dimov
Bacteria 2022, 1(3), 183-190; https://doi.org/10.3390/bacteria1030014 - 7 Sep 2022
Viewed by 4206
Abstract
In this study, we used the sequence of the aac(6′)-Ii gene, which is responsible for the intrinsic low-level aminoglycoside resistance of Enterococcus faecium, to design novel species-specific primers. Two oligonucleotide pairs named EF_200 and EF_120 were designed, generating amplification products with sizes [...] Read more.
In this study, we used the sequence of the aac(6′)-Ii gene, which is responsible for the intrinsic low-level aminoglycoside resistance of Enterococcus faecium, to design novel species-specific primers. Two oligonucleotide pairs named EF_200 and EF_120 were designed, generating amplification products with sizes of 200 bp and 120 bp, respectively. They were successfully applied for the identification of various isolates of clinical or environmental origins in both pure cultures and complex food samples. The obtained results indicated that both primer pairs permitted the highly specific, simple, fast and inexpensive detection of E. faecium isolates. Full article
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22 pages, 26063 KiB  
Article
Comparative Genomics and In Silico Evaluation of Genes Related to the Probiotic Potential of Bifidobacterium breve 1101A
by Juan Valdez-Baez, Francielly Morais Rodrigues da Costa, Anne Cybelle Pinto Gomide, Rodrigo Profeta, Alessandra Lima da Silva, Thiago de Jesus Sousa, Marcus Vinícius Canário Viana, Rodrigo Bentes Kato, Monique Ferrary Americo, Andria dos Santos Freitas, Rodrigo Dias de Oliveira Carvalho, Bertram Brenig, Flaviano Santos Martins, Flavia Aburjaile and Vasco Azevedo
Bacteria 2022, 1(3), 161-182; https://doi.org/10.3390/bacteria1030013 - 13 Jul 2022
Cited by 7 | Viewed by 5818
Abstract
Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. [...] Read more.
Bifidobacterium breve is among the first microorganisms colonizing the intestinal tract in humans and is a predominant species in the gut microbiota of newborns and children. This bacterium is widely used in the probiotic industry due to its capacity to improve host health. The search for new targets with probiotic properties is an increasing trend with the help of next-generation sequencing as they facilitate the characterization of the bacterial features. B. breve 1101A was isolated from the faeces of healthy children in Brazil and therefore could play a protective role in the gut. To investigate the beneficial properties of this strain, the present study performed a comprehensive characterization of the genetic features involved in the bacterium resistance and adaptation to gastrointestinal conditions, production of nutrients, and immunomodulatory compounds. Furthermore, this study carried out the prediction of genomic elements (plasmids, prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes) to evaluate the safety of B. breve 1101A. A comparative genomics approach using 45 B. breve complete genomes based on pangenome and phylogenomic analysis was also performed to identify specific genes in B. breve 1101A. The prediction of genetic elements, possibly safety-related, did not detect plasmids, but only one incomplete prophage, two non-functional CRISPR systems, and seven genomic islands. Additionally, three antibiotic resistance genes were identified: ileS (resistance to mupirocin), rpoB, and erm(X). In the comparative genomic analysis, the pangenome was revealed to be open, and B. breve 1101A presented 63 unique genes associated with several processes, such as transmembrane transport, membrane components, DNA processes, and carbohydrate metabolism. In conclusion, B. breve 1101A is potentially safe and well-adapted for intestinal disorder therapeutics, although the role of its unique genetic repertoire needs further investigation. Full article
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25 pages, 37006 KiB  
Article
Genomic Characterization of Lactiplantibacillus plantarum Strains Possessing Differential Antiviral Immunomodulatory Activities
by Leonardo Albarracin, Fernanda Raya Tonetti, Kohtaro Fukuyama, Yoshihito Suda, Binghui Zhou, Ayelén A. Baillo, Silvina Fadda, Lucila Saavedra, Shoichiro Kurata, Elvira M. Hebert, Haruki Kitazawa and Julio Villena
Bacteria 2022, 1(3), 136-160; https://doi.org/10.3390/bacteria1030012 - 6 Jul 2022
Cited by 8 | Viewed by 3702
Abstract
Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the [...] Read more.
Lactiplantibacillus plantarum strains are used in the food industry for their probiotic properties. Some of these bacteria have immunomodulatory effects on the host and are able to improve resistance against different pathogens, including viruses. However, to date, the bacterial genes involved in the immunomodulatory effect are not known. In this work, the complete genomes of L. plantarum MPL16, CRL1506, CRL681 and TL2766 were used to perform comparative genomics with the aim of identifying the genes involved in their differential immunomodulatory effects. L. plantarum WCFS1, a strain with proven probiotic activity, was also used for comparisons. The analysis of the genes involved in the metabolic pathways of the five strains did not reveal differences in the metabolism of amino acids, lipids, nucleotides, cofactors and vitamins, nor in the genes associated with energy metabolism or the biosynthesis of lipoproteins and teichoic acids. However, differences were found between the five strains when considering carbohydrate metabolism pathways, particularly in the presence/absence of glycosylhydrolases and glycosyltransferases. In addition, a great variability was detected in the predicted surface proteins of each L. plantarum strain. These results suggest that the surface molecules expressed in the different strains of L. plantarum could be involved in their differential ability to modulate the innate antiviral immune response. Full article
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