Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection

Abstract

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.

Figure 1. Bacterial Divisions and Their Lineages Detected in the Zebrafish Digestive Tract, Mouse Cecum, and Human Colon

(A) Summary of shared and distinct bacterial divisions in the zebrafish, mouse, and human gut microbiota (data from this study; Rawls et al., 2004; Ley et al., 2005; Eckburg et al., 2005; Bäckhed et al., 2005). Divisions found in the normal gut microbiota of each host are indicated (+). (B–D) Phylogenetic trees constructed from enumeration studies of the zebrafish digestive tract (B), mouse cecal (C), and human colonic (D) microbiotas. The zebrafish data are 1456 16S rRNA gene sequences derived from adult CONV-R C32 fish. The mouse data are 2196 sequences from adult CONV-R C57Bl/6J mice and their mothers (Ley et al., 2005). The human dataset contains 2989 bacterial 16S rRNA sequences from colonic mucosal biopsies and a fecal sample obtained from a healthy adult (Eckburg et al., 2005). Within a given panel, yellow lines indicate lineages unique to the host, blue lines indicate lineages that are shared by at least one other host, while black lines indicate lineages that are absent from the host. The scale bar indicates 10% pairwise 16S rRNA sequence divergence.

Figure 2. Comparison of Input and Output Communities following Reciprocal Transplantation of Gut Microbiotas in Gnotobiotic Zebrafish and Mice

Tree based on pairwise differences between the following bacterial communities (weighted UniFrac metric, based on a 6379 sequence tree; Lozupone and Knight, 2005): (1) CONV-R zebrafish digestive tract microbiota (conventionally raised zebrafish, red); (2) CONV-R mouse cecal microbiota (conventionally raised mice, yellow); (3) output community from the cecal contents of ex-GF mice that had been colonized with a normal zebrafish microbiota (Z-mice, blue); (4) output community from the digestive tracts from ex-GF zebrafish that had been colonized with a normal mouse microbiota (M-zebrafish, green); and (5) a control soil community that served as an outgroup (Soil; Axelrood et al., 2002). The distance p value for this entire UniFrac tree (UniFrac P, the probability that there are more unique branches than expected by chance, using 1000 iterations) was found to be <0.001, assigning high confidence to the overall structure of the UniFrac tree. 16S rRNA library names are shown next to their respective branch (see Table S1 for additional details about these libraries). The relative abundance of different bacterial divisions within these different communities (replicate libraries pooled) is shown in pie charts with dominant divisions highlighted.

Figure 3. Similarity Indices for Pairwise Comparisons of Communities Defined as Assemblages of Phylotypes Computed at Levels of %ID Ranging from 86%ID to 100%ID and Compared at Each %ID Threshold using the Chao-Jaccard Abundance-Based Similarity Index

Abbreviations: zebrafish into mouse, CONV-R zebrafish compared to Z-mouse microbiotas; mouse into zebrafish, CONV-R mouse compared to M-zebrafish microbiotas; zebrafish into zebrafish, CONV-R zebrafish compared to Z-zebrafish microbiotas (data from Rawls et al., 2004); mouse into mouse, CONV-R mouse compared to M-mouse microbiotas (data from Bäckhed et al., 2004). Similarity indices range from 0 (no overlap in composition) to 1 (identical communities).

Figure 4. Identifying a Common Response of the Germ-free Mouse Distal Small Intestine to Colonization with Mouse and Zebrafish Gut Microbial Communities

(A) Summary of results of GeneChip analysis of the ileal transcriptome in GF mice versus mice colonized for 14 days with a mouse cecal microbiota (M-mice versus GF; red lines) or a normal zebrafish digestive tract microbiota (Z-mice versus GF; blue lines). Note that only a subset of all Affymetrix GeneChip probe sets are annotated by Ingenuity Pathway Analysis (IPA). Supplemental tables containing GeneChip probe set and IPA gene information are indicated. IPA reveals metabolic pathways (panel B; Table S12) and molecular functions (panel C; Table S13) that are significantly enriched (p < 0.05) in the host response to each community. The seven most significant metabolic pathways and the four most significant signaling pathways from the M-mice versus GF mice comparison (red bars) are shown along with corresponding data from the Z-mice versus GF mice comparison (blue bars). (Not shown: the 275 IPA-annotated mouse genes regulated by the mouse microbiota but unchanged by the zebrafish digestive tract microbiota were significantly enriched for components of ERK/MAPK, SAPK/JNK, antigen presentation, and the pentose phosphate pathways [Table S9]. In contrast, the 300 IPA-annotated mouse genes regulated by the zebrafish microbiota but unchanged by the mouse microbiota were enriched for components of glutamate and arginine/proline metabolism, ketone body synthesis/degradation, plus β-adrenergic signaling pathways [Table S11]).

Figure 5. qRT-PCR Assays of the Responses of Germ-free Zebrafish to Colonization with Individual Culturable Members of the Zebrafish and Mouse Gut Microbiotas

Expression levels of serum amyloid a (saa), myeloperoxidase (mpo), fasting-induced adipose factor (fiaf), carnitine palmitoyltransferase 1a (cpt1a), and proliferating cell nuclear antigen (pcna) were assessed using RNA extracted from the pooled digestive tracts of 6dpf zebrafish inoculated since 3dpf with a CONV-R zebrafish microbiota (Z-zebrafish), a CONV-R mouse microbiota (M-zebrafish), a consortium of seven primary isolates (Consortium), a primary Enterococcus isolate (M2E1F06), a primary Staphylococcus isolate (M2E1A04), a primary Citrobacter isolate (T1E1C07), a primary Aeromonas isolate (T1E1A06), a primary Plesiomonas isolate (T1N1D03), a primary Shewanella isolate (T1E1C05), a primary Escherichia isolate (M1N2G03), an Escherichia coli type strain (E. coli MG1655), an Aeromonas hydrophila type strain (A. hydrophila ATCC35654), a Pseudomonas aeruginosa type strain (P. aeruginosa PAO1), or 0.1 µg/ml P. aeruginosa LPS (P. aeruginosa LPS). Data from biological duplicate pools (≥10 animals per pool) were normalized to 18S rRNA levels and results expressed as mean fold-difference compared to GF controls ± SEM. S phase cells were quantified in the intestinal epithelium of 6dpf zebrafish colonized since 3dpf with a CONV-R zebrafish microbiota (Z-zebrafish), a consortium of seven primary isolates (Consortium), or individual species. The percentage of all intestinal epithelial cells in S phase was scored using antibodies directed against BrdU, following incubation in BrdU for 24 hr prior to sacrifice. Data are expressed as the mean of two independent experiments ± SEM (n = 9–15 five micron-thick transverse sections scored per animal, ≥7 animals analyzed per experiment). ***, p < 0.0001; **, p < 0.001; *, p < 0.05.