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Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ - Microbiome (2015)

Bottom Line: The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format.FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota.This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.

View Article: PubMed Central - PubMed

Affiliation: Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.

ABSTRACT

Background: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT.

Results: Here we report on short- and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated using FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP.

Conclusions: Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.

No MeSH data available.


Related in: MedlinePlus

Changes in fecal microbial communities after FMT. Relative abundance of sequences classified to the level of bacterial phyla before and after FMT in patient fecal samples. Samples after FMT indicated with dashed line. See key at right.
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Fig3: Changes in fecal microbial communities after FMT. Relative abundance of sequences classified to the level of bacterial phyla before and after FMT in patient fecal samples. Samples after FMT indicated with dashed line. See key at right.

Mentions: While overall fecal microbial communities were dramatically altered following FMT, we also examined the effects of the procedure on the abundance and dynamics of individual bacterial taxa within the four original CDI patients. As shown previously [2-8], the relative abundance of bacterial phyla in patient fecal samples shifted substantially following FMT, with relative decreases in Proteobacteria and relative increases in Bacteroidetes and Firmicutes (Figure 3). These Proteobacteria are primarily the order Enterobacteriales, which were also substantially decreased in relative abundance following FMT (Figure 4A).Figure 3


Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ - Microbiome (2015)

Changes in fecal microbial communities after FMT. Relative abundance of sequences classified to the level of bacterial phyla before and after FMT in patient fecal samples. Samples after FMT indicated with dashed line. See key at right.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4378022&req=5

Fig3: Changes in fecal microbial communities after FMT. Relative abundance of sequences classified to the level of bacterial phyla before and after FMT in patient fecal samples. Samples after FMT indicated with dashed line. See key at right.
Mentions: While overall fecal microbial communities were dramatically altered following FMT, we also examined the effects of the procedure on the abundance and dynamics of individual bacterial taxa within the four original CDI patients. As shown previously [2-8], the relative abundance of bacterial phyla in patient fecal samples shifted substantially following FMT, with relative decreases in Proteobacteria and relative increases in Bacteroidetes and Firmicutes (Figure 3). These Proteobacteria are primarily the order Enterobacteriales, which were also substantially decreased in relative abundance following FMT (Figure 4A).Figure 3

Bottom Line: The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format.FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota.This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.

View Article: PubMed Central - PubMed

Affiliation: Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.

ABSTRACT

Background: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT.

Results: Here we report on short- and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated using FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP.

Conclusions: Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.

No MeSH data available.


Related in: MedlinePlus