Extensive horizontal gene transfer in cheese-associated bacteria

Bonham, Kevin S.; Wolfe, Benjamin E.; Dutton, Rachel J

doi:10.7554/elife.22144

Cited by 94 publications

(76 citation statements)

References 82 publications

(109 reference statements)

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“…Probiotics, cheeses, and other dairy products are rich in microorganisms that could participate in genetic exchange processes with resident organisms in the gut microbiome [26]. In this sense, the fact that cheese and dairy industries are hot spots for genetic exchange [33] highlights the possible impact of foods in the human gut microbiome.…”

Section: Direct Impact Of Transfers Occurring In Human Microbiomesmentioning

confidence: 99%

“…Several studies show that HGT among fungi plays an important role in their adaptation to cheese producing environment [48,49]. In addition, a recent study shows that 130 bacterial species associated with cheese production have horizontally transferred genes [33], suggesting that horizontal exchange is frequent between bacteria in the cheese producing environment. Knowing that cheese industry can be an HGT hotspot should alert us about possible consequences of an unintended and occasional transfer of pathogenic determinants or antimicrobial resistances in this environment.…”

Section: Indirect Impact Of Hgt In Bacterial Communities Living In Humentioning

confidence: 99%

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Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it

Boto

Pineda

2019

The FEBS Journal

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Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.

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Section: Direct Impact Of Transfers Occurring In Human Microbiomesmentioning

confidence: 99%

Section: Indirect Impact Of Hgt In Bacterial Communities Living In Humentioning

confidence: 99%

Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it

Boto

Pineda

2019

The FEBS Journal

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“…On the other hand, phages can likely act as vectors for horizontal gene transfer, which is a common phenomenon in the dairy production [22]. Here we could uncover evidence for such an active phage system by assembling the bacterial host genome, as well as the inserted prophage and lytic phage.…”

Section: Discussionmentioning

confidence: 82%

“…As a consequence, whey cultures recurrently encounter considerable environmental changes (e.g., temperature, pH, and redox potential). These harsh culture conditions are known to lead to widespread horizontal gene transfer (HGT) events in the production of fermented foods [22].…”

Section: Introductionmentioning

confidence: 99%

Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

Somerville

Lutz

Schmid

et al. 2018

Preprint

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BackgroundComplete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled-genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been shown so far. Natural whey starter cultures (NWCs) are used in the production of cheese and represent low complex microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon-based metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. ResultsTwo NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using Pacific Biosciences Sequel, Oxford Nanopore Technologies MinION and Illumina MiSeq platforms. We achieved the complete assembly of all dominant bacterial genomes from these low complex NWCs, which was corroborated by a 16S rRNA based amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial genomes, we could also assemble several bacterial plasmids as well as phages and a corresponding prophage. Biologically relevant insights could be uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing third generation, long-read sequencing data able to span intragenomic as well as intergenomic repeats. ConclusionsHere, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low complex NWC's based on whole metagenomics shotgun sequencing data.This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omic analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.

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“…Surveillance of AMR is currently based on the isolation of indicator microorganisms and their phenotypic characterisation, but this culture-dependent approach does not provide complete information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Metagenomics is a powerful tool that allows culture-independent analysis of complex microbial communities and thus has potential applications in AMR surveillance (Bonham et al, 2017;Fl orez et al, 2017;Walsh et al, 2017). It can provide access to all the genetic resources in a given environmental niche, which is essential for obtaining the genomes of fastidious or non-culturable microorganisms.…”

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confidence: 99%

Risk assessment of antimicrobial resistance along the food chain through culture‐independent methodologies

Likotrafiti¹,

Oniciuc²,

Prieto³

et al. 2018

EFS2

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Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life‐threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food‐related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture‐independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.

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Extensive horizontal gene transfer in cheese-associated bacteria

Cited by 94 publications

References 82 publications

Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it

Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it

Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

Risk assessment of antimicrobial resistance along the food chain through culture‐independent methodologies

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