Companies seek food safety using a microbiome approach

Beans, Carolyn

doi:10.1073/pnas.1719373114

Cited by 3 publications

(2 citation statements)

References 3 publications

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“…There is increasing awareness of the impact microbiota have on all aspects of life; the carbon fixation by phototrophs in the oceans (52,53), the health of bees that pollinate plants (54), the production and safety of food (55), and various aspects of human health among others (56). Along with this increased appreciation of microbiomes comes a richer understanding of the roles parasites play; viruses infect hosts throughout the tree of life (57), with bacteriophages, recently re-emerging as a potential tool in biotechnology and the treatment of human disease.…”

Section: Discussionmentioning

confidence: 99%

DominantVibrio choleraephage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

Hays

Seed

2019

Preprint

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AbstractBacteriophages and their bacterial hosts are locked in a dynamic evolutionary arms race. Phage satellites, selfish genomic islands which exploit both host bacterium and target phage, further complicate the evolutionary fray. One such tripartite system involves the etiological agent of the diarrheal disease cholera – Vibrio cholerae, the predominant phage isolated from cholera patients – ICP1, and a phage satellite – PLE. When ICP1 infects V. cholerae harboring the integrated PLE genome, PLE accelerates host lysis, spreading the PLE while completely blocking phage production protecting V. cholerae at the population level. Here we identify a single PLE gene, lidI, sufficient to mediate accelerated lysis during ICP1 infection and demonstrate that LidI functions through disrupting lysis inhibition – an understudied outcome of phage infection when phages vastly outnumber their hosts. This work identifies ICP1-encoded holin and antiholin genes teaA and arrA respectively, that mediate this first example of lysis inhibition outside the T-even coliphages. Through lysis inhibition disruption, LidI is sufficient to limit the number of progeny phage produced from an infection. Consequently, this disruption bottlenecks ICP1 evolution as probed by recombination and CRISPR-Cas targeting assays. These studies link novel characterization of the classic phenomenon of lysis inhibition with a conserved protein in a dominant phage satellite, highlighting the importance of lysis timing during infection and parasitization, as well as providing insight into the populations, relationships, and evolution of bacteria, phages, and phage satellites in nature.ImportanceWith increasing awareness of microbiota impacting human health comes intensified examination of, not only bacteria and the bacteriophages that prey upon them, but also the mobile genetic elements (MGEs) that mediate interactions between them. Research is unveiling evolutionary strategies dependent on sensing the milieu: quorum sensing impacts phage infection, phage teamwork overcomes bacterial defenses, and abortive infections sacrifice single cells protecting populations. Yet, the first discovered environmental sensing by phages, known as lysis inhibition (LIN), has only been studied in the limited context of T-even coliphages. Here we characterize LIN in the etiological agent of the diarrheal disease cholera, Vibrio cholerae, infected by a phage ubiquitous in clinical samples. Further, we show that a specific MGE, the phage satellite PLE, collapses LIN with a conserved protein during its anti-phage program. The insights gleaned from this work add to our expanding understanding of microbial fitness in natural contexts beyond the canonical bacterial genome and into the realm of antagonistic evolution driven by phages and satellites.

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Section: Discussionmentioning

confidence: 99%

DominantVibrio choleraephage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

Hays

Seed

2019

Preprint

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“…High throughput sequencing using shorter regions of 16S rDNA produce more read depth and allow an effective analysis of complex bacterial species bypassing the need of culturing and limitations thereof. Next generation sequencing is being widely used for analyzing microbial diversity of great variety of environments, including soil 17,18 , sea 19,20 , air 21 and other agriculture food samples 22 . In this study Illumina sequencing based NGS using single 16S phylogenetic marker was employed to identify the microorganisms present in commercial aquaculture probiotics.…”

Section: Introductionmentioning

confidence: 99%

Assessing the Microbial Quality of Commercial Aquaculture Probiotics by Next Generation Sequencing Revealed Faecal Bacteria and Bacteria of Public Health Significance

Joseph¹,

K.S²,

T.R³

et al. 2021

Preprint

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There is an increasing trend in the application of probiotics in aquaculture as an environment friendly alternative to antibiotics for the control and treatment of diseases. The microbiome of commercial aquaculture probiotics were evaluated using NGS to understand the microbial species composition vis-à-vis the label on the probiotic product. Bacteria belonging to 12 bacterial species stated on the labels of five probiotics were absent. The sequence reads of the microorganisms declared on the label ranged from 0.28-79 % for the probiotics tested while the rest were contaminants. The number of contaminant bacteria varied from 2 to 15 for the tested products. All products were found to have at least one bacterial species that were potentially pathogenic or of fecal origin. To our knowledge this is the first study that utilized the potential of NGS to assess the microbial quality of commercial aquaculture probiotics providing novel insights in understanding the microbial composition of probiotic products which are otherwise difficult to identify. It is proposed that probiotic products shall be approved for use in aquaculture after determining the performance efficiency by in vivo trails in farms, analysis of bacterial composition and concentration which shall be displayed on product labels.

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Recent trends in molecular techniques for food pathogen detection

Rao

Arora

2020

Chemical Analysis of Food

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Companies seek food safety using a microbiome approach

Cited by 3 publications

References 3 publications

DominantVibrio choleraephage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

DominantVibrio choleraephage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

Assessing the Microbial Quality of Commercial Aquaculture Probiotics by Next Generation Sequencing Revealed Faecal Bacteria and Bacteria of Public Health Significance

Recent trends in molecular techniques for food pathogen detection

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