Nucleotide 9-mers characterize the type II diabetic gut metagenome.
Identifieur interne : 001223 ( PubMed/Corpus ); précédent : 001222; suivant : 001224Nucleotide 9-mers characterize the type II diabetic gut metagenome.
Auteurs : Balázs Szalkai ; Vince GrolmuszSource :
- Genomics [ 1089-8646 ] ; 2016.
English descriptors
- KwdEn :
- Biomarkers (chemistry), Case-Control Studies, Diabetes Mellitus, Type 2 (microbiology), Female, Gastrointestinal Microbiome, Gastrointestinal Tract (microbiology), Humans, Male, Metagenome, Nucleotides (chemistry), Nucleotides (isolation & purification), Obesity (microbiology), Thinness (microbiology).
- MESH :
- chemical , chemistry : Biomarkers, Nucleotides.
- chemical , isolation & purification : Nucleotides.
- microbiology : Diabetes Mellitus, Type 2, Gastrointestinal Tract, Obesity, Thinness.
- Case-Control Studies, Female, Gastrointestinal Microbiome, Humans, Male, Metagenome.
Abstract
Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research.
DOI: 10.1016/j.ygeno.2016.02.007
PubMed: 26945643
Links to Exploration step
pubmed:26945643Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Nucleotide 9-mers characterize the type II diabetic gut metagenome.</title>
<author><name sortKey="Szalkai, Balazs" sort="Szalkai, Balazs" uniqKey="Szalkai B" first="Balázs" last="Szalkai">Balázs Szalkai</name>
<affiliation><nlm:affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: szalkai@pitgroup.org.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Grolmusz, Vince" sort="Grolmusz, Vince" uniqKey="Grolmusz V" first="Vince" last="Grolmusz">Vince Grolmusz</name>
<affiliation><nlm:affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: grolmusz@pitgroup.org.</nlm:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2016">2016</date>
<idno type="RBID">pubmed:26945643</idno>
<idno type="pmid">26945643</idno>
<idno type="doi">10.1016/j.ygeno.2016.02.007</idno>
<idno type="wicri:Area/PubMed/Corpus">001223</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001223</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Nucleotide 9-mers characterize the type II diabetic gut metagenome.</title>
<author><name sortKey="Szalkai, Balazs" sort="Szalkai, Balazs" uniqKey="Szalkai B" first="Balázs" last="Szalkai">Balázs Szalkai</name>
<affiliation><nlm:affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: szalkai@pitgroup.org.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Grolmusz, Vince" sort="Grolmusz, Vince" uniqKey="Grolmusz V" first="Vince" last="Grolmusz">Vince Grolmusz</name>
<affiliation><nlm:affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: grolmusz@pitgroup.org.</nlm:affiliation>
</affiliation>
</author>
</analytic>
<series><title level="j">Genomics</title>
<idno type="eISSN">1089-8646</idno>
<imprint><date when="2016" type="published">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biomarkers (chemistry)</term>
<term>Case-Control Studies</term>
<term>Diabetes Mellitus, Type 2 (microbiology)</term>
<term>Female</term>
<term>Gastrointestinal Microbiome</term>
<term>Gastrointestinal Tract (microbiology)</term>
<term>Humans</term>
<term>Male</term>
<term>Metagenome</term>
<term>Nucleotides (chemistry)</term>
<term>Nucleotides (isolation & purification)</term>
<term>Obesity (microbiology)</term>
<term>Thinness (microbiology)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Biomarkers</term>
<term>Nucleotides</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>Nucleotides</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Diabetes Mellitus, Type 2</term>
<term>Gastrointestinal Tract</term>
<term>Obesity</term>
<term>Thinness</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Case-Control Studies</term>
<term>Female</term>
<term>Gastrointestinal Microbiome</term>
<term>Humans</term>
<term>Male</term>
<term>Metagenome</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research. </div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26945643</PMID>
<DateCompleted><Year>2016</Year>
<Month>12</Month>
<Day>13</Day>
</DateCompleted>
<DateRevised><Year>2016</Year>
<Month>12</Month>
<Day>30</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8646</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>107</Volume>
<Issue>4</Issue>
<PubDate><Year>2016</Year>
<Month>Apr</Month>
</PubDate>
</JournalIssue>
<Title>Genomics</Title>
<ISOAbbreviation>Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Nucleotide 9-mers characterize the type II diabetic gut metagenome.</ArticleTitle>
<Pagination><MedlinePgn>120-3</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ygeno.2016.02.007</ELocationID>
<ELocationID EIdType="pii" ValidYN="Y">S0888-7543(16)30015-5</ELocationID>
<Abstract><AbstractText>Discoveries of new biomarkers for frequently occurring diseases are of special importance in today's medicine. While fully developed type II diabetes (T2D) can be detected easily, the early identification of high risk individuals is an area of interest in T2D, too. Metagenomic analysis of the human bacterial flora has shown subtle changes in diabetic patients, but no specific microbes are known to cause or promote the disease. Moderate changes were also detected in the microbial gene composition of the metagenomes of diabetic patients, but again, no specific gene was found that is present in disease-related and missing in healthy metagenome. However, these fine differences in microbial taxon- and gene composition are difficult to apply as quantitative biomarkers for diagnosing or predicting type II diabetes. In the present work we report some nucleotide 9-mers with significantly differing frequencies in diabetic and healthy intestinal flora. To our knowledge, it is the first time such short DNA fragments have been associated with T2D. The automated, quantitative analysis of the frequencies of short nucleotide sequences seems to be more feasible than accurate phylogenetic and functional analysis, and thus it might be a promising direction of diagnostic research. </AbstractText>
<CopyrightInformation>Copyright © 2016 Elsevier Inc. All rights reserved.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Szalkai</LastName>
<ForeName>Balázs</ForeName>
<Initials>B</Initials>
<AffiliationInfo><Affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary. Electronic address: szalkai@pitgroup.org.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Grolmusz</LastName>
<ForeName>Vince</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>PIT Bioinformatics Group, Eötvös University, H-1117 Budapest, Hungary; Uratim Ltd., H-1118 Budapest, Hungary. Electronic address: grolmusz@pitgroup.org.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2016</Year>
<Month>03</Month>
<Day>03</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Genomics</MedlineTA>
<NlmUniqueID>8800135</NlmUniqueID>
<ISSNLinking>0888-7543</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D015415">Biomarkers</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D009711">Nucleotides</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D015415" MajorTopicYN="N">Biomarkers</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016022" MajorTopicYN="N">Case-Control Studies</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003924" MajorTopicYN="N">Diabetes Mellitus, Type 2</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000069196" MajorTopicYN="N">Gastrointestinal Microbiome</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D041981" MajorTopicYN="N">Gastrointestinal Tract</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D054892" MajorTopicYN="Y">Metagenome</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009711" MajorTopicYN="N">Nucleotides</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009765" MajorTopicYN="N">Obesity</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013851" MajorTopicYN="N">Thinness</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Biomarkers</Keyword>
<Keyword MajorTopicYN="N">G-C content</Keyword>
<Keyword MajorTopicYN="N">Metagenome</Keyword>
<Keyword MajorTopicYN="N">Oligomers</Keyword>
<Keyword MajorTopicYN="N">Short nucleotide sequences</Keyword>
<Keyword MajorTopicYN="N">Tetranucleotides</Keyword>
<Keyword MajorTopicYN="N">Type II diabetes</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year>
<Month>09</Month>
<Day>21</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2016</Year>
<Month>02</Month>
<Day>25</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2016</Year>
<Month>02</Month>
<Day>26</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2016</Year>
<Month>3</Month>
<Day>7</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2016</Year>
<Month>3</Month>
<Day>8</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2016</Year>
<Month>12</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">26945643</ArticleId>
<ArticleId IdType="pii">S0888-7543(16)30015-5</ArticleId>
<ArticleId IdType="doi">10.1016/j.ygeno.2016.02.007</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001223 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001223 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Corpus |type= RBID |clé= pubmed:26945643 |texte= Nucleotide 9-mers characterize the type II diabetic gut metagenome. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:26945643" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |