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Reshaping the gut microbiome with bacterial transplantation and antibiotic intake
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class="contributor-list" id="contrib-group-1"> <li class="contributor" id="contrib-1" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Chaysavanh+Manichanh&sortspec=date&submit=Submit">Chaysavanh Manichanh</a></span><a id="xref-aff-1-1" class="xref-aff" href="#aff-1">1</a><span class="xref-sep">,</span><a id="xref-fn-1-1" class="xref-corresp" href="#fn-1">5</a>, </li> <li class="contributor" id="contrib-2" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Jens+Reeder&sortspec=date&submit=Submit">Jens Reeder</a></span><a id="xref-aff-2-1" class="xref-aff" href="#aff-2">2</a>, </li> <li class="contributor" id="contrib-3" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Prudence+Gibert&sortspec=date&submit=Submit">Prudence Gibert</a></span><a id="xref-aff-1-2" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-4" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Encarna+Varela&sortspec=date&submit=Submit">Encarna Varela</a></span><a id="xref-aff-1-3" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-5" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Marta+Llopis&sortspec=date&submit=Submit">Marta Llopis</a></span><a id="xref-aff-1-4" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-6" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Maria+Antolin&sortspec=date&submit=Submit">Maria Antolin</a></span><a id="xref-aff-1-5" class="xref-aff" href="#aff-1">1</a>, </li> <li class="contributor" id="contrib-7" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Roderic+Guigo&sortspec=date&submit=Submit">Roderic Guigo</a></span><a id="xref-aff-3-1" class="xref-aff" href="#aff-3">3</a>, </li> <li class="contributor" id="contrib-8" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Rob+Knight&sortspec=date&submit=Submit">Rob Knight</a></span><a id="xref-aff-2-2" class="xref-aff" href="#aff-2">2</a><span class="xref-sep">,</span><a id="xref-aff-4-1" class="xref-aff" href="#aff-4">4</a> and </li> <li class="last" id="contrib-9"><span class="name"><a class="name-search" href="/search?author1=Francisco+Guarner&sortspec=date&submit=Submit">Francisco Guarner</a></span><a id="xref-aff-1-6" class="xref-aff" href="#aff-1">1</a></li> </ol> <ol class="affiliation-list"> <li class="aff"><a id="aff-1" name="aff-1"></a><address> <sup>1</sup>Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain; </address> </li> <li class="aff"><a id="aff-2" name="aff-2"></a><address> <sup>2</sup>Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA; </address> </li> <li class="aff"><a id="aff-3" name="aff-3"></a><address> <sup>3</sup>Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain; </address> </li> <li class="aff"><a id="aff-4" name="aff-4"></a><address> <sup>4</sup>Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA </address> </li> </ol> <ol class="corresp-list"></ol> </div> <div class="section abstract" id="abstract-1" itemprop="description"> <h2>Abstract</h2> <p id="p-3">The intestinal microbiota consists of over 1000 species, which play key roles in gut physiology and homeostasis. Imbalances in the composition of this bacterial community can lead to transient intestinal dysfunctions and chronic disease states. Understanding how to manipulate this ecosystem is thus essential for treating many disorders. In this study, we took advantage of recently developed tools for deep sequencing and phylogenetic clustering to examine the long-term effects of exogenous microbiota transplantation combined with and without an antibiotic pretreatment. In our rat model, deep sequencing revealed an intestinal bacterial diversity exceeding that of the human gut by a factor of two to three. The transplantation produced a marked increase in the microbial diversity of the recipients, which stemmed from both capture of new phylotypes and increase in abundance of others. However, when transplantation was performed after antibiotic intake, the resulting state simply combined the reshaping effects of the individual treatments (including the reduced diversity from antibiotic treatment alone). Therefore, lowering the recipient bacterial load by antibiotic intake prior to transplantation did not increase establishment of the donor phylotypes, although some dominant lineages still transferred successfully. Remarkably, all of these effects were observed after 1 mo of treatment and persisted after 3 mo. Overall, our results indicate that the indigenous gut microbial composition is more plastic that previously anticipated. However, since antibiotic pretreatment counterintuitively interferes with the establishment of an exogenous community, such plasticity is likely conditioned more by the altered microbiome gut homeostasis caused by antibiotics than by the primary bacterial loss. </p> </div> <div class="section fn-group" id="fn-group-1"> <h2>Footnotes</h2> <ul> <li class="fn-corresp" id="fn-1"> <p id="p-1"><a class="rev-xref" href="#xref-fn-1-1">↵</a><span class="fn-label">5</span> Corresponding author. </p> <p id="p-2">E-mail <span class="em-link"><span class="em-addr">cmanicha{at}gmail.com</span></span>; fax 34-934-894-032. </p> </li> <li class="fn" id="fn-2"> <p id="p-4">[Supplemental material is available online at <a href="http://www.genome.org">http://www.genome.org</a>. The sequencing data from this study have been submitted to the NCBI Sequence Read Archive (<a href="http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi">http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi</a>) under accession no. SRA020673.] </p> </li> <li class="fn" id="fn-3"> <p id="p-5">Article published online before print. Article and publication date are at <a href="http://www.genome.org/cgi/doi/10.1101/gr.107987.110">http://www.genome.org/cgi/doi/10.1101/gr.107987.110</a>. </p> </li> </ul> </div> <ul class="history-list"> <li xmlns:hwp="http://schema.highwire.org/Journal" class="received" hwp:start="2010-03-19"><span class="received-label">Received </span>March 19, 2010. </li> <li xmlns:hwp="http://schema.highwire.org/Journal" class="accepted" hwp:start="2010-07-16"><span class="accepted-label">Accepted </span>July 16, 2010. </li> </ul> <ul class="copyright-statement"> <li class="fn" id="copyright-statement-1">Copyright © 2010 by Cold Spring Harbor Laboratory Press</li> </ul><span class="highwire-journal-article-marker-end"></span></div> <div class="social-bookmarking"> <ul class="social-bookmark-links"> <li class="social-bookmarking-item social-bookmarking-item-citeulike"><a 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