RT Journal
A1 Manichanh, Chaysavanh
A1 Reeder, Jens
A1 Gibert, Prudence
A1 Varela, Encarna
A1 Llopis, Marta
A1 Antolin, Maria
A1 Guigo, Roderic
A1 Knight, Rob
A1 Guarner, Francisco
T1 Reshaping the gut microbiome with bacterial transplantation and antibiotic intake
JF Genome Research 
JO Genome Research 
YR 2010 
FD October 01 
VO 20 
IS 10 
SP 1411 
OP 1419 
DO 10.1101/gr.107987.110 
UL http://genome.cshlp.org/content/20/10/1411.abstract 
AB 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.