Complete Genes May Pass from Food to Human Blood
Publication Date
July 30, 2013
Journal
PLOS ONE
Authors
Sándor Spisák, Norbert Solymosi, Péter Ittzés, András Bodor, et al
Volume
8
Issue
7
Pages
e69805
DOI
https://dx.plos.org/10.1371/journal.pone.0069805
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0069805
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23936105
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728338
Europe PMC
http://europepmc.org/abstract/MED/23936105
Web of Science
000323114200046
Scopus
84880796060
Mendeley
http://www.mendeley.com/research/complete-genes-pass-food-human-blood
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Mendeley | Further Information

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According to the standard paradigm large macromolecules consumed with food cannot pass directly to the circulatory system. During digestion proteins and DNA are thought to be degraded into small constituents, amino acids and nucleic acids, respectively, and then absorbed by a complex active process and distributed to various parts of the body through the circulation system. Here, based on the analysis of over 1000 human samples from four independent studies, we report evidence that meal-derived DNA fragments which are large enough to carry complete genes can avoid degradation and through an unknown mechanism enter the human circulation system. In one of the blood samples the relative concentration of plant DNA is higher than the human DNA. The plant DNA concentration shows a surprisingly precise log-normal distribution in the plasma samples while non-plasma (cord blood) control sample was found to be free of plant DNA.", "link"=>"http://www.mendeley.com/research/complete-genes-pass-food-human-blood", "reader_count"=>181, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>8, "Student > Doctoral Student"=>13, "Researcher"=>44, "Student > Ph. D. Student"=>33, "Student > Postgraduate"=>3, "Other"=>15, "Student > Master"=>18, "Student > Bachelor"=>29, "Lecturer"=>2, "Professor"=>12}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>8, "Student > Doctoral Student"=>13, "Researcher"=>44, "Student > Ph. D. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1137095"], "description"=>"<p>Small gray dots indicate the counts of alignments at individual nucleotide positions, darker shades are the result of several overlapping points. The orange line is the smoothed coverage of the tomato chloroplast, while the short gray dash indicates the average coverage level of the human genome for the same sample.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "chloroplast", "ibd"], "article_id"=>759831, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coverage_of_the_tomato_chloroplast_in_the_IBD_sample_/759831", "title"=>"Coverage of the tomato chloroplast in the IBD sample.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137096"], "description"=>"<p>The gray spikes shows the counts of alignments at individual nucleotide positions (vertical scale is logarithmic). 27742 nucleotide positions of the total 180852 are covered. There are two regions around 100,000 and 135,000 where the coverage is more than 10 times than at other parts of the chloroplast. These are the regions where the ribosomal RNA genes are found which share very similar sequence with other chloroplasts and bacterial genomes. Indeed if we BLAST all the 1634 reads that matched the chloroplast genomes against the NCBI reference sequence database, 733 of them also match various bacterial genomes, but 897 does not match any other organisms, just plants. Removing those alignments that match bacterial genomes too, (gray spikes) makes the distribution more uniform.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "rapa", "chloroplast", "pileup", "drp000446"], "article_id"=>759832, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.g002", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Brassica_rapa_chloroplast_coverage_pileup_for_the_DRP000446_study_/759832", "title"=>"Brassica rapa chloroplast coverage pileup for the DRP000446 study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137097"], "description"=>"<p>It (black dots) can be fitted with log-normal distribution (red curve) above the sensitivity cutoff (0.35). The gray shaded band is the result of the simulation of 300 realizations of the log-normal process with taking into account the varying sizes of the samples. Among the independent samples (larger dots), the ones from patients with inflammatory diseases (IBD, DRP000446) have the largest concentration. For the SRP016573 sample only the maternal plasma concentration is shown, full blood samples with 0.001 ppm and 0.004 ppm and cord blood samples with zero alignments are omitted from the figure.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "cumulative", "dna", "900"], "article_id"=>759833, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_cumulative_distribution_of_plant_DNA_amount_for_over_900_subjects_/759833", "title"=>"The cumulative distribution of plant DNA amount for over 900 subjects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137098"], "description"=>"<p>From the total 903 subjects the ones with the largest number of matches are shown (only the plant genomes with more than 50, and only the subjects with more than 10 matching reads), the rows are the plant species, the columns are the samples. The automatic clustering recovers the related plant species and the subjects can be also grouped by the food types.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "heatmap", "shows", "chloroplast", "matching", "reads", "srp009039"], "article_id"=>759834, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_This_heatmap_shows_the_number_of_chloroplast_matching_reads_on_a_scale_for_the_SRP009039_study_/759834", "title"=>"This heatmap shows the number of chloroplast matching reads on a scale for the SRP009039 study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137099"], "description"=>"<p>The chloroplast genomes of these species were obtained from the NCBI archive and their presence was tested in the sequenced human samples.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "accession", "numbers", "names"], "article_id"=>759835, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.t001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_accession_numbers_and_names_of_the_plants_/759835", "title"=>"The accession numbers and names of the plants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137100"], "description"=>"<p>BLAST against the complete NCBI reference sequence database confirms that the chloroplast matching reads identified by the NGS alignment software Bowtie match only plant genomes and just in very few cases mammal genomes. The bacterial alignments are partly the result of the chloroplasts' genetic homology to them or may indicate the presence of circulating bacterial DNA. Among the IBD fractions, the one with largest DNA fragment size has the largest concentration.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "reads", "ones", "matching", "chloroplast", "genome"], "article_id"=>759836, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.t002", "stats"=>{"downloads"=>7, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_initial_number_of_sequence_reads_and_the_ones_matching_the_chloroplast_genome_collection_/759836", "title"=>"The initial number of sequence reads and the ones matching the chloroplast genome collection.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-30 07:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1137101"], "description"=>"<p>Though some reads which were identified by the aligner software (Bowtie) can be fitted to other species like bacteria, most of them match plants only.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Digestive system", "Digestive physiology", "Digestive functions", "genomics", "Genome analysis tools", "Genome scans", "Genome-wide association studies", "Comparative genomics", "Genome sequencing", "metagenomics", "reads", "samples", "chloroplast", "matching"], "article_id"=>759837, "categories"=>["Biological Sciences"], "users"=>["Sándor Spisák", "Norbert Solymosi", "Péter Ittzés", "András Bodor", "Dániel Kondor", "Gábor Vattay", "Barbara K. Barták", "Ferenc Sipos", "Orsolya Galamb", "Zsolt Tulassay", "Zoltan Szallasi", "Simon Rasmussen", "Thomas Sicheritz-Pontén", "Søren Brunak", "Béla Molnár", "István Csabai"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069805.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_sequence_reads_in_the_samples_and_the_number_and_ratio_of_chloroplast_matching_ones_/759837", "title"=>"The number of sequence reads in the samples and the number and ratio of chloroplast matching ones.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-30 07:51:18"}

PMC Usage Stats | Further Information

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Relative Metric

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