Genome analysis of probiotic bacteria for antibiotic resistance genes

Fatahi-Bafghi, Mehdi; Naseri, Sara; Alizehi, Ali

doi:10.1007/s10482-021-01703-7

Cited by 14 publications

(12 citation statements)

References 81 publications

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“…However, antibiotic resistance gene, ermX , was detected in the genome of strain TA-R-1 T , which encodes an enzyme capable of modifying the DNA sequence of the 23S rRNA gene through methylation, resulting in resistance to macrolides, lincosamides, and streptogramin B ( Chen et al, 2007 ). A previous study analyzing the whole genomes of 126 probiotics uncovered several resistance genes on plasmids, which can be transferred to other bacteria ( Fatahi-Bafghi et al, 2022 ). However, we did not find plasmids carrying the transferred gene in the genome of the strain TA-R-1 T .…”

Section: Discussionmentioning

confidence: 99%

Genome insight and probiotic potential of three novel species of the genus Corynebacterium

et al. 2023

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Three bacterial strains, B5-R-101T, TA-R-1T, and BL-R-1T, were isolated from the feces of a healthy Korean individual. Cells of these strains were Gram-stain-positive, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped, and non-motile. They were able to grow within a temperature range of 10–42°C (optimum, 32–37°C), at a pH range of 2.0–10.0 (optimum, pH 5.5–8.0), and at NaCl concentration of 0.5–10.5% (w/v). All the three strains exhibited 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities ranging from 58 ± 1.62 to 79 ± 1.46% (% inhibition). These strains survived in lower pH (2.0) and in 0.3% bile salt concentration for 4 h. They did not show hemolytic activity and exhibited antimicrobial activity against pathogenic bacteria, such as Escherichia coli, Acinetobacter baumannii, Staphylococcus aureus, and Salmonella enterica. The genomic analysis presented no significant concerns regarding antibiotic resistance or virulence gene content, indicating these strains could be potential probiotic candidates. Phylogenetic analysis showed that they belonged to the genus Corynebacterium, with 98.5–99.0% 16S rRNA gene sequence similarities to other members of the genus. Their major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The abundant cellular fatty acids were C16:0, C18:1ω9c, and anteiso-C19:0. Genomic analysis of these isolates revealed the presence of genes necessary for their survival and growth in the gut environment, such as multi-subunit ATPases, stress response genes, extracellular polymeric substance biosynthesis genes, and antibacterial genes. Furthermore, the genome of each strain possessed biosynthetic gene clusters with antioxidant and antimicrobial potentials, including terpenes, saccharides, polyketides, post-translationally modified peptides (RIPPs), and non-ribosomal peptides (NRPs). In silico DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values were lower than the thresholds to distinguish novel species. Based on phenotypic, genomic, phylogenomic, and phylogenetic analysis, these potential probiotic strains represent novel species within the genus Corynebacterium, for which the names Corynebacterium intestinale sp. nov. (type strain B5-R-101T = CGMCC 1.19408T = KCTC 49761T), Corynebacterium stercoris sp. nov. (type strain TA-R-1T = CGMCC 1.60014T = KCTC 49742T), and Corynebacterium faecium sp. nov. (type strain BL-R-1T = KCTC 49735T = TBRC 17331T) are proposed.

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Section: Discussionmentioning

confidence: 99%

Genome insight and probiotic potential of three novel species of the genus Corynebacterium

et al. 2023

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Section: Facilitating the Trafficking Of Antimicrobial Resistant Gene...mentioning

confidence: 99%

“…Given the availability of increasing number of complete probiotic bacteria genomes and the development of bioinformatic tools such as ARG-ANNOT and Resfinder for the detection of existing and putative ARGs, a recent in silico study has analyzed 126 complete probiotic bacterial genomes and detected many ARGs some of which, are known to be transferable [ 187 ]. The authors found that the tetracycline resistant gene tet(W) found in both Bifidobacterium and Lactobacillus was the most abundant [ 187 ]. Another study that analyzed 47 shotgun sequencing datasets from probiotic samples consisting of 20 singles isolates and 27 metagenomes, detected more than 70 ARGs that operate through known mechanisms such as antibiotic efflux, inactivation or reduced permeability, and antibiotic target alteration, protection, or replacement [ 188 ].…”

Section: Facilitating the Trafficking Of Antimicrobial Resistant Gene...mentioning

confidence: 99%

Accounting for the health risk of probiotics

Liu,

Zhao,

Wong

2024

Heliyon

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“…Additionally, the significant routes for the spread of antibiotic-resistant probiotic bacteria are food chain and gastrointestinal tract (GIT) [ 2 , 10 ]. So these microbes can function as vectors for the transfer of antimicrobial resistance genes from foodstuff to living organisms [ 3 , 11 , 12 ]. Probiotics are considered as beneficial bacterial category of lactic acid bacteria, and safety of probiotics may be compromised if they function as a vector for transmittance of antimicrobial genes to potential pathogenic bacteria [ 6 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…So these microbes can function as vectors for the transfer of antimicrobial resistance genes from foodstuff to living organisms [ 3 , 11 , 12 ]. Probiotics are considered as beneficial bacterial category of lactic acid bacteria, and safety of probiotics may be compromised if they function as a vector for transmittance of antimicrobial genes to potential pathogenic bacteria [ 6 , 12 ]. Frequency of misusing antibiotics among women of childbearing age in developing world including Pakistan is much higher because of ineffectiveness of satisfactory guidelines on antibiotics [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Unveiling the Antibiotic Susceptibility and Antimicrobial Potential of Bacteria from Human Breast Milk of Pakistani Women: An Exploratory Study

Saeed

Ali

Yasmin

et al. 2023

BioMed Research International

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Background. Human life quality and expectancy have increased dramatically over the past 5 decades because of improvements in nutrition and antibiotic’s usage fighting against infectious diseases. Yet, it was soon revealed that the microbes adapted to develop resistance to any of the drugs that were used. Recently, there is great concern that commensal bacteria from food and the gastrointestinal tract of humans and animals could act as a reservoir for antibiotic resistance genes. Methodology. This study was intended for evaluating the phenotypic antibiotic resistance/sensitivity profiles of probiotic bacteria from human breast milk and evaluating the inhibitory effect of the probiotic bacteria against both Gram-negative and Gram-positive bacteria. Results. The results point out that some of the isolated bacteria were resistant to diverse antibiotics including gentamycin, imipenem, trimethoprim sulfamethoxazole, and nalidixic acid. Susceptibility profile to certain antibiotics like vancomycin, tetracycline, ofloxacin, chloramphenicol, streptomycin, rifampicin, and bacitracin was also observed. The antimicrobial qualities of cell-free supernatants of some probiotic bacteria inhibited the growth of indicator bacteria. Also, antimicrobial properties of the probiotic bacteria from the present study attributed to the production of organic acid, bacterial adhesion to hydrocarbons (BATH), salt aggregation, coaggregation with pathogens, and bacteriocin production. Some isolated bacteria from human milk displayed higher hydrophobicity in addition to intrinsic probiotic properties like Gram-positive classification, catalase-negative activity, resistance to gastric juice (pH 2), and bile salt (0.3%) concentration. Conclusion. This study has added to the data of the antibiotic and antimicrobial activity of some probiotic bacteria from some samples of Pakistani women breast milk. Probiotic bacteria are usually considered to decrease gastrointestinal tract diseases by adhering to the gut epithelial and reducing population of pathogens and in the case of Streptococcus lactarius MB622 and Streptococcus salivarius MB620 in terms of hydrophobicity and exclusion of indicator pathogenic strains.

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Genome analysis of probiotic bacteria for antibiotic resistance genes

Cited by 14 publications

References 81 publications

Genome insight and probiotic potential of three novel species of the genus Corynebacterium

Genome insight and probiotic potential of three novel species of the genus Corynebacterium

Accounting for the health risk of probiotics

Unveiling the Antibiotic Susceptibility and Antimicrobial Potential of Bacteria from Human Breast Milk of Pakistani Women: An Exploratory Study

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