Screening of potential probiotic lactic acid bacteria with antimicrobial properties and selection of superior bacteria for application as biocontrol using machine learning models

Sadeghi, Mahsa; Panahi, Bahman; Mazlomi, Atefeh; Hejazi, Mohammad Amin; Nami, Yousef

doi:10.1016/j.lwt.2022.113471

Cited by 44 publications

(27 citation statements)

References 27 publications

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“…Phages infect the bacterial hosts and highjack the host-cell machinery in the lytic (or virulent) lifestyle for replicating as well as destroying the host, which consequently led to decrease of living bacteria account, and even fermentation and production failure (Nami et al, 2021;Sadeghi et al, 2022). Other detrimental effects of LAB lysis by phages are the decline of acidification, texture development, and flavor enhancement.…”

Section: Introductionmentioning

confidence: 99%

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

2022

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Clustered regularly interspaced short palindromic repeats (CRISPR) together with their CRISPR-associated (Cas) genes are widely distributed in prokaryotes that provide an adaptive defense mechanism against foreign invasive DNA. There is relatively little knowledge about the CRISPR-Cas diversity and evolution in Lactobacillus brevis strains. Therefore, in this study, a genome-mining approach was employed to investigate the diversity and occurrence of the CRISPR-Cas system in 83 L. brevis strains. Moreover, trans-activating CRISPR RNA (tracrRNA) and protospacer adjacent motif (PAM) as pivotal elements for the successful targeting and inference of phages by the subtype II CRISPR-Cas systems were surveyed. Finally, evolutionary paths of L. brevis strains under selective pressure from foreign invasive DNA such as plasmids and phages of studied strains were surveyed using acquisition and deletion events analysis of spacers. A total of 127 confirmed CRISPRs were identified, which were distributed in 69 strains. Among strains with confirmed CRISPRs, 35 strains only contained one CRISPR locus, 23 strains contained two CRISPR loci, and 12 strains contained three to six CRISPR loci. L. brevis strains frequently harbor more than one CRISPR system. Analysis of confirmed CRISPR arrays showed that 31 out of 127 confirmed CRISPRs included Cas genes which were categorized as one of the II-A, II-C, and I-E subtypes. Analysis of subtype II-A spacers reflected divergent evolution for 18 strains into 16 unique groups. Additional analysis of spacer sequences also confirmed the implication of characterizing CRISPR-Cas systems in targeting of phages and plasmids. The current study highlighted the potential of utilizing CRISPR spacer polymorphism in genotyping lactobacillus strains. Moreover, it provides deep insights into the occurrence, diversity, and functional impacts of the CRISPR-Cas system in L. brevis strains.

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Section: Introductionmentioning

confidence: 99%

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

2022

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“…The broad antibacterial spectrum of probiotics and their strong antibacterial activity against pathogens are their important functional properties 8 . In addition to working on the principle of exclusion of competitors and using immune-stimulators to combat illness, probiotic bacteria produce digestive enzymes that improve digestion, thereby improving host stress tolerance and health 6 .…”

Section: Introductionmentioning

confidence: 99%

Probiotic potential characterization and clustering using unsupervised algorithms of lactic acid bacteria from saltwater fish samples

Mazlumi

Panahi

Hejazi

et al. 2022

Sci Rep

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This research aimed to isolate lactic acid bacteria from the bowel of saltwater fish to assess their potential probiotic properties. Nineteen isolates of LAB including Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Lactobacillus acidophilus, Levilactobacillus brevis, Pediococcus pentosaceus, and Pediococcus acidilactici were recognized using molecular tools. All the isolates survived in the simulated conditions of the GI tract. Auto-aggregation ranged from 01.3 ± 0.5 to 82.6 ± 1.4% and hydrophobicity with toluene ranged from 3.7 ± 1.6 to 69.4 ± 1.3%, while the range of hydrophobicity with xylene was from 02.2 ± 1.6 to 56.4 ± 2.1%. All the isolates of lactobacilli, pediococci, enterococci, and lactococci indicated variable sensitivity and resistance towards clinical antibiotics. Non-neutralized cell free supernatant of isolates F12 and F15 showed antimicrobial activity against all the 8 evaluated enteric pathogens. Cluster analysis of identified potential probiotic bacteria based on heat-map and PCA methods also highlighted the priority of isolates F3, F7, F12, and F15 as bio-control agents in fishery industry. The findings of this study may essentially contribute to the understanding of the probiotic potential of LAB in saltwater fish, in order to access their probiotic characterization for use as biocontrol in fishery.

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“…Converging this application in the presented context of probiotics in clinical depression, machine learning paves the way for integrating microbial bases in depressive disorder from the consortia of the characteristic, endophenotypic, neurobiological, and genetic censuses to optimize management and treatment options using probiotics. Although this remains a futuristic vision, a handful of studies have begun to explore the machine learning application in microbiome, probiotics, and precision psychiatry [ 104 , 106 , 218 , 219 , 220 , 221 ].…”

Section: Potential Microbial-based Approach In the Clinical Managemen...mentioning

confidence: 99%

A Microbial-Based Approach to Mental Health: The Potential of Probiotics in the Treatment of Depression

Johnson

Letchumanan

Thum³

et al. 2023

Nutrients

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Probiotics are currently the subject of intensive research pursuits and also represent a multi-billion-dollar global industry given their vast potential to improve human health. In addition, mental health represents a key domain of healthcare, which currently has limited, adverse-effect prone treatment options, and probiotics may hold the potential to be a novel, customizable treatment for depression. Clinical depression is a common, potentially debilitating condition that may be amenable to a precision psychiatry-based approach utilizing probiotics. Although our understanding has not yet reached a sufficient level, this could be a therapeutic approach that can be tailored for specific individuals with their own unique set of characteristics and health issues. Scientifically, the use of probiotics as a treatment for depression has a valid basis rooted in the microbiota-gut-brain axis (MGBA) mechanisms, which play a role in the pathophysiology of depression. In theory, probiotics appear to be ideal as adjunct therapeutics for major depressive disorder (MDD) and as stand-alone therapeutics for mild MDD and may potentially revolutionize the treatment of depressive disorders. Although there is a wide range of probiotics and an almost limitless range of therapeutic combinations, this review aims to narrow the focus to the most widely commercialized and studied strains, namely Lactobacillus and Bifidobacterium, and to bring together the arguments for their usage in patients with major depressive disorder (MDD). Clinicians, scientists, and industrialists are critical stakeholders in exploring this groundbreaking concept.

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Screening of potential probiotic lactic acid bacteria with antimicrobial properties and selection of superior bacteria for application as biocontrol using machine learning models

Cited by 44 publications

References 27 publications

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

Probiotic potential characterization and clustering using unsupervised algorithms of lactic acid bacteria from saltwater fish samples

A Microbial-Based Approach to Mental Health: The Potential of Probiotics in the Treatment of Depression

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