Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium
Identifieur interne : 000179 ( Pmc/Checkpoint ); précédent : 000178; suivant : 000180Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium
Auteurs : Sandra Appelt [France] ; Fabrice Armougom [France] ; Matthieu Le Bailly [France] ; Catherine Robert [France] ; Michel Drancourt [France]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Paleomicrobiological investigations of a 14th-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by
Url:
DOI: 10.1371/journal.pone.0088376
PubMed: 24586319
PubMed Central: 3938422
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>Paleomicrobiological investigations of a 14<sup>th</sup>
-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by <italic>ad hoc</italic>
PCR – sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were <italic>Proteobacteria</italic>
, <italic>Gemmatimonadetes</italic>
, <italic>Actinobacteria</italic>
and <italic>Bacteroidetes</italic>
. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to <italic>Proteobacteria</italic>
, <italic>Firmicutes</italic>
, <italic>Actinobacteria</italic>
and <italic>Chlamydia</italic>
. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites <italic>Trichuris</italic>
and <italic>Ascaris</italic>
and systemic pathogens <italic>Bartonella</italic>
and <italic>Bordetella</italic>
. This study adds knowledge to gut microbiota in medieval times.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24586319</article-id>
<article-id pub-id-type="pmc">3938422</article-id>
<article-id pub-id-type="publisher-id">PONE-D-13-39648</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0088376</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Evolutionary biology</subject>
<subj-group><subject>Paleontology</subject>
<subj-group><subject>Micropaleontology</subject>
<subject>Paleobiology</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group><subject>Microbiology</subject>
<subj-group><subject>Bacterial pathogens</subject>
</subj-group>
</subj-group>
<subj-group><subject>Paleontology</subject>
<subj-group><subject>Micropaleontology</subject>
<subject>Paleobiology</subject>
</subj-group>
</subj-group>
<subj-group><subject>Plant science</subject>
<subj-group><subject>Botany</subject>
<subj-group><subject>Flora</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Earth sciences</subject>
<subj-group><subject>Paleontology</subject>
<subj-group><subject>Micropaleontology</subject>
<subject>Paleobiology</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Medicine</subject>
<subj-group><subject>Infectious diseases</subject>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Social and behavioral sciences</subject>
<subj-group><subject>Anthropology</subject>
<subj-group><subject>Biological anthropology</subject>
<subject>Paleoanthropology</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium</article-title>
<alt-title alt-title-type="running-head">Middle Ages European Coprolite Flora</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Appelt</surname>
<given-names>Sandra</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Armougom</surname>
<given-names>Fabrice</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Le Bailly</surname>
<given-names>Matthieu</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Robert</surname>
<given-names>Catherine</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Drancourt</surname>
<given-names>Michel</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<addr-line>Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France</addr-line>
</aff>
<aff id="aff2"><label>2</label>
<addr-line>Centre national de la recherche scientifique UMR 6249 Chrono-Environnement, Franche-Comté Université, Besançon, France</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Bourtzis</surname>
<given-names>Kostas</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>International Atomic Energy Agency, Austria</addr-line>
</aff>
<author-notes><corresp id="cor1">* E-mail: <email>Michel.Drancourt@medicine.univ-mrs.fr</email>
</corresp>
<fn fn-type="conflict"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con"><p>Conceived and designed the experiments: MD. Performed the experiments: SA. Analyzed the data: FA CR. Contributed reagents/materials/analysis tools: MLB. Wrote the paper: SA MD.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>28</day>
<month>2</month>
<year>2014</year>
</pub-date>
<volume>9</volume>
<issue>2</issue>
<elocation-id>e88376</elocation-id>
<history><date date-type="received"><day>27</day>
<month>9</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>6</day>
<month>1</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-year>2014</copyright-year>
<copyright-holder>Appelt et al</copyright-holder>
<license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<abstract><p>Paleomicrobiological investigations of a 14<sup>th</sup>
-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by <italic>ad hoc</italic>
PCR – sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were <italic>Proteobacteria</italic>
, <italic>Gemmatimonadetes</italic>
, <italic>Actinobacteria</italic>
and <italic>Bacteroidetes</italic>
. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to <italic>Proteobacteria</italic>
, <italic>Firmicutes</italic>
, <italic>Actinobacteria</italic>
and <italic>Chlamydia</italic>
. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites <italic>Trichuris</italic>
and <italic>Ascaris</italic>
and systemic pathogens <italic>Bartonella</italic>
and <italic>Bordetella</italic>
. This study adds knowledge to gut microbiota in medieval times.</p>
</abstract>
<funding-group><funding-statement>No external funding for this study.</funding-statement>
</funding-group>
<counts><page-count count="8"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>France</li>
</country>
<region><li>Provence-Alpes-Côte d'Azur</li>
</region>
<settlement><li>Besançon</li>
<li>Marseille</li>
</settlement>
<orgName><li>Université d'Aix-Marseille</li>
</orgName>
</list>
<tree><country name="France"><noRegion><name sortKey="Appelt, Sandra" sort="Appelt, Sandra" uniqKey="Appelt S" first="Sandra" last="Appelt">Sandra Appelt</name>
</noRegion>
<name sortKey="Armougom, Fabrice" sort="Armougom, Fabrice" uniqKey="Armougom F" first="Fabrice" last="Armougom">Fabrice Armougom</name>
<name sortKey="Drancourt, Michel" sort="Drancourt, Michel" uniqKey="Drancourt M" first="Michel" last="Drancourt">Michel Drancourt</name>
<name sortKey="Le Bailly, Matthieu" sort="Le Bailly, Matthieu" uniqKey="Le Bailly M" first="Matthieu" last="Le Bailly">Matthieu Le Bailly</name>
<name sortKey="Robert, Catherine" sort="Robert, Catherine" uniqKey="Robert C" first="Catherine" last="Robert">Catherine Robert</name>
</country>
</tree>
</affiliations>
</record>
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