Human intestinal microbiota: Characterization of a simplified and stable gnotobiotic rat model

Abstract

The study of host microbe interactions is hampered by the complexity and inter-individual variability of the human gut microbiota. Therefore, a simplified human intestinal microbiota (SIHUMI) consisting of seven bacterial species was introduced into germfree rats. Species selection was based on numerical importance and fermentative abilities in the human gut. Association of the rats with the SIHUMI (Anaerostipes caccae, Bacteroides thetaiotaomicron, Bifidobacterium longum, Blautia producta, Clostridium ramosum, Escherichia coli and Lactobacillus plantarum) resulted in increased faecal concentrations of short chain fatty acids compared to germfree animals. Since the faecal butyrate concentration was low (0.9 ± 0.5 µmol/g dry matter) the SIHUMI was complemented with Clostridium butyricum. This extended bacterial community (SIHUMIx) led to an increased faecal butyrate concentration of 1.5 ± 0.7 µmol/g dry matter. Besides forming SCFA, the SIHUMIx was capable of degrading mucins, β-aspartylglycine and bilirubin. These features are characteristic of conventional animals but not observed in germfree animals. Dietary interventions with modifications in fibre and fat content led to changes in the proportion of community members. The relative increase of one member of this community in response to a high-fat diet reflects the situation reported for obese mice and human subjects. The strength of the model communities is their remarkable stability over time and their easy transfer to the offspring.

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

“…Narrowing measurements to the 18-species consortium MIBAC-1, which can be used as a proxy for native mouse gut ecosystems, revealed coverages of 55-75% (PFAM and sequence homologues) and 20% (close sequence matches). Minimal consortia of bacteria already exist in the literature, but strains were selected based on educated guesses or for specific purposes and either originated from the human intestinal tract or are not easily available 26,27,37 . In contrast, the minimal bacteriome presented here contains strains that originate from the mouse intestine, is publicly available, was selected on the basis of comprehensive sequence-based approaches, and was overall characterized by a higher coverage of mouse faecal metagenomes.…”

“…First, a local database was created of all miBC genomes and the metagenomes in a presence/absence binary code (1/0) of protein families (PFAM). Deterministic incremental selection of best fitted genomes was performed to assess coverage of the metagenomes by all miBC species (n = 76), or by species included in the minimal bacteriome MIBAC-1 (n = 18; this study), SIHUMI (n = 8) 27 and ASF (n = 8) 26 . Second, ORFs in metagenomic contigs were selected and initial annotation was carried out with prokka 64 .…”

“…Next, we investigated coverage of the mouse metagenomes (n = 17) by comparing miBC and the minimal bacteriome MIBAC-1 with consortia from the literature, that is, the ASF 26 and the Simplified Human Intestinal Microbiota (SIHUMI) 27 . Coverage analysis included not only the PFAM approach, but also protein sequence coverage by BLAST analysis (that is, independent of functional annotation) for determination of both homology (≥80% length coverage, E < 10 −5 ) and close sequence match (≥80% both coverage and sequence similarity).…”

High-fat diet alters gut microbiota physiology in mice

“…Finally, the conversion of bilirubin to urobilinogen is considered to be a specific feature of the gut microbiota, especially Clostridium spp. (Becker et al, 2011). Thus, higher levels of urobilinogen and its oxidized product urobilin in the cecum of HF mice (i) testify to dietinduced functional alterations of the microbial ecosystem, (ii) may be related to the observed HFinduced increase in phylotypes within the Clostridiales, an order that includes known converters of bilirubin, and (iii) could explain the appearance of the FT-IR spectral features attributed to aromatic and heteroaromatic ring vibrations in the cecum of HF mice.…”

Rodent models to study the relationships between mammals and their bacterial inhabitants

“…50 A step up in complexity, the association of GF animals with 5-15 species provides a more complex yet simple enough model to investigate host-microbe and microbe-microbe interactions. A simplified human intestinal microbiota consisting of seven bacterial species harbored in gnotobiotic rats 51 showed metabolic functions comparable to conventional rats with respect to previously proposed mucosa-associated characteristics: 52 production of short-chain fatty acids, conversion of bilirubin to urobilinogen, degradation of mucins and β-aspartylglycine, and inactivation of trypsin. Genomes of the selected bacterial community are publicly available, which has facilitated (as already mentioned) further studies at the molecular level.…”