Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

Abstract

Background: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits.

Methods: We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients.

Results: Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8 weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems.

Conclusions: The analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.

Keywords: Colonization; Fecal microbiota transplantation; Metagenome-assembled genomes; Metagenomics.

Fig. 1

Distribution of MAGs across samples and HMP metagenomes. a The 92 MAGs and their level of detection in four donor samples (four inner circles) as well as two recipients (R01 and R02) before FMT (pre-FMT), 4 weeks after FMT (W4), and 8 weeks after FMT (W8). Rectangles with red and blue colors in donor and recipient layers indicate the level of detection of a given MAG in a given sample. The outermost two layers display the genus- and order-level taxonomy for each MAG. Selections in a represent four groups of MAGs based on their distribution patterns: group I with 20 MAGs that colonized both recipients, group II with 11 MAGs that colonized only R01, group III with 8 MAGs that colonized only R02, and finally, group IV with 13 MAGs that colonized neither recipient. b The detection for each contig in two example MAGs summarized to a single detection value in a. c The coverage of each nucleotide position in two example contigs from the MAGs displayed in b. d The prevalence of MAGs in groups I and IV across 151 HMP gut metagenomes and detection of MAG 54 (group I) and MAG 26 (group IV) in HMP gut metagenomes as two examples

Fig. 2

Canonical correspondence analysis of functions in four groups of MAGs. The 39 significant functional subcategories are shown

Fig. 3

Similarity between donor and recipient samples before and after FMT. Non-metric multidimensional scaling based on mean coverage of 92 MAGs and based on microbial community profiles from this study and 151 HMP metagenomes at the genus level of short reads annotated by MetaPhlAn. Clustering employed average linkage with Bray-Curtis similarity index on square-root normalized values. Labels represent the recipients (R01, R02) before FMT (pre-FMT), 4 weeks (W4) and 8 weeks after FMT (W8). Gray circles represent HMP metagenomes. Panel a displays changes in recipient microbial community profiles after FMT based on coverage values of donor MAGs. Panel b displays the organization of samples based on the genus-level taxonomy of all short metagenomic reads in each sample. In contrast, Panel c displays the genus organization of samples based on the genus-level taxonomy of only short metagenomic reads that do not match donor MAGs