In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases

Surachat, Komwit; Sangket, Unitsa; Deachamag, Panchalika; Chotigeat, Wilaiwan

doi:10.1371/journal.pone.0183548

Cited by 31 publications

(21 citation statements)

References 90 publications

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“…Similar to our study, it has been observed that bacteriocins encoded by Lactobacillus are species, strain, and origin dependent (59). The different classes of bacteriocins detected from L. paracasei 3E were similar to those observed with the probiotic strain L. paracasei SD1 (60). Expression of these bacteriocins may have led to L. paracasei 3E being one of the strongest inhibitors of M. haemolytica (ZOI, Ͼ22 mm).…”

Section: Discussionsupporting

confidence: 88%

Development of Bacterial Therapeutics against the Bovine Respiratory Pathogen Mannheimia haemolytica

Amat

Timsit

Baines

et al. 2019

Appl Environ Microbiol

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Bovine respiratory disease (BRD) is a major cause of morbidity and mortality in beef cattle. Recent evidence suggests that commensal bacteria of the bovine nasopharynx have an important role in maintaining respiratory health by providing colonization resistance against pathogens. The objective of this study was to screen and select bacterial therapeutic candidates from the nasopharynxes of feedlot cattle to mitigate the BRD pathogen Mannheimia haemolytica. In a stepwise approach, bacteria (n = 300) isolated from the nasopharynxes of 100 healthy feedlot cattle were identified and initially screened (n = 178 isolates from 12 different genera) for growth inhibition of M. haemolytica. Subsequently, selected isolates were evaluated for the ability to adhere to bovine turbinate (BT) cells (n = 47), compete against M. haemolytica for BT cell adherence (n = 15), and modulate gene expression in BT cells (n = 10). Lactobacillus strains had the strongest inhibition of M. haemolytica, with 88% of the isolates (n =33) having inhibition zones ranging from 17 to 23 mm. Adherence to BT cells ranged from 3.4 to 8.0 log10 CFU per 105 BT cells. All the isolates tested in competition assays reduced M. haemolytica adherence to BT cells (32% to 78%). Among 84 bovine genes evaluated, selected isolates upregulated expression of interleukin 8 (IL-8) and IL-6 (P < 0.05). After ranking isolates for greatest inhibition, adhesion, competition, and immunomodulation properties, 6 Lactobacillus strains from 4 different species were selected as the best candidates for further development as intranasal bacterial therapeutics to mitigate M. haemolytica infection in feedlot cattle. IMPORTANCE Bovine respiratory disease (BRD) is a significant animal health issue impacting the beef industry. Current BRD prevention strategies rely mainly on metaphylactic use of antimicrobials when cattle enter feedlots. However, a recent increase in BRD-associated bacterial pathogens that are resistant to metaphylactic antimicrobials highlights a pressing need for the development of novel mitigation strategies. Based upon previous research showing the importance of respiratory commensal bacteria in protecting against bronchopneumonia, this study aimed to develop bacterial therapeutics that could be used to mitigate the BRD pathogen Mannheimia haemolytica. Bacteria isolated from the respiratory tracts of healthy cattle were characterized for their inhibitory, adhesive, and immunomodulatory properties. In total, 6 strains were identified as having the best properties for use as intranasal therapeutics to inhibit M. haemolytica. If successful in vivo, these strains offer an alternative to metaphylactic antimicrobial use in feedlot cattle for mitigating BRD.

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Section: Discussionsupporting

confidence: 88%

Development of Bacterial Therapeutics against the Bovine Respiratory Pathogen Mannheimia haemolytica

Amat

Timsit

Baines

et al. 2019

Appl Environ Microbiol

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“…The procedure was highly selective for large DNA fragments while excluding smaller plasmid DNAs from the sequencing reaction. Often, the PacBio sequencing was regarded as the platform providing complete genomic information as both chromosome and large plasmids, usually with the size larger than 10 kb, were detected 7,8 . Thus, the presence of small plasmids and their associated risk were not determined.…”

Section: Resultsmentioning

confidence: 99%

“…To the best of our knowledge, despite suggestions on the issues that should be investigated for microbial safety assessment 6,17 , no clear procedural guideline have been provided. Despite several studies reported on microbial safety assessements 7,11,14,27 , no consensual procedure agreement can be observed. Therefore, we would like to propose the guideline for conducting the microbial safety evaluation using the whole-genome analysis as follow:…”

Section: Safety Conclusion Of L Plantarum Bcc9546mentioning

confidence: 87%

“…The accurate taxonomic placement is crucial for the identification of possible risk associated with the taxon. Following the protocol used in this study, the problem of misidentification or inability to distinguish between closely related species as seen in the identification based on biochemical assays and 16 S rRNA gene analysis 7,11 can be alleviated.…”

Section: Pacbiomentioning

confidence: 99%

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Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis

Chokesajjawatee

Santiyanont

Chantarasakha

et al. 2020

Sci Rep

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The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have been suggested, no methodological detail nor procedural guideline have been published. Herein, we propose a detailed protocol on microbial strain safety assessment via whole-genome sequence analysis. A starter culture employed in traditional fermented pork production, nham, namely Lactobacillus plantarum BCC9546, was used as an example. The strain’s whole-genome was sequenced through several next-generation sequencing techniques. Incomplete plasmid information from the PacBio sequencing platform and shorter chromosome size from the hybrid Oxford Nanopore-Illumina platform were noted. The methods for 1) unambiguous species identification using 16S rRNA gene and average nucleotide identity, 2) determination of virulence factors and undesirable genes, 3) determination of antimicrobial resistance properties and their possibility of transfer, and 4) determination of antimicrobial drug production capability of the strain were provided in detail. Applicability of the search tools and limitations of databases were discussed. Finally, a procedural guideline for the safety assessment of microbial strains via whole-genome analysis was proposed.

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“…We found that eight Lactobacillus isolates could reduce C. albicans hyphae formation, and L. paracasei 28.4 showed the greatest amount of reduction. This fact could be due to the Lactobacillus production of antimicrobial molecules such as bacteriocins, since the reduction of the pH was not significant [46,47].…”

Section: Discussionmentioning

confidence: 99%

Lactobacillus paracasei 28.4 reduces in vitro hyphae formation of Candida albicans and prevents the filamentation in an experimental model of Caenorhabditis elegans

Barros

Scorzoni

Ribeiro

et al. 2018

Microbial Pathogenesis

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The objective of this study was to evaluate the influence of microbe-microbe interactions to identify a strain of Lactobacillus that could reduce the filamentation of Candida albicans ATCC 18804 using in vitro and in vivo models. Thus presenting a probiotic effect against the fungal pathogen. First, we analyzed the ability of 25 clinical isolates of Lactobacillus to reduce filamentation in C. albicans in vitro. We found that L. paracasei isolate 28.4 exhibited the greatest reduction of C. albicans hyphae (p = 0.0109). This reduction was confirmed by scanning electron microscopy analysis. The influence of C. albicans filamentation was found to be contributed through reduced gene expression of filament associated genes (TEC1 and UME6). In an in vivo study, prophylactic provisions with L. paracasei increased the survival of Caenorhabditis elegans worms infected with C. albicans (p = 0.0001) by 29%. Prolonged survival was accompanied by the prevention of cuticle rupture of 27% of the worms by filamentation of C. albicans, a phenotype that is characteristic of C. albicans killing of nematodes, compared to the control group. Lactobacillus paracasei isolate 28.4 reduced the filamentation of C. albicans in vitro by negatively regulating the TEC1 and UME6 genes that are essential for the production of hyphae. Prophylactic provision of Lactobacillus paracasei 28.4 protected C. elegans against candidiasis in vivo. L. paracasei 28.4 has the potential to be employed as an alternative method to control candidiasis.

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In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases

Cited by 31 publications

References 90 publications

Development of Bacterial Therapeutics against the Bovine Respiratory Pathogen Mannheimia haemolytica

Development of Bacterial Therapeutics against the Bovine Respiratory Pathogen Mannheimia haemolytica

Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis

Lactobacillus paracasei 28.4 reduces in vitro hyphae formation of Candida albicans and prevents the filamentation in an experimental model of Caenorhabditis elegans

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