Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

Abstract

The human gut is colonized by a complex microbiota with multiple benefits. Although the surfaceattached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

“…Numerous systems have been developed and allowed to study the impact of prebiotics, probiotics, and antibiotics on the gut microbiota, or even the microbial composition at colon microenvironments. [26][27][28][29] The system used here has the particularity to maintain anaerobia due to the metabolic activity of the microorganisms constituting the microbiota: therefore, it leads to atmospheres that are variable among fermenters and whose constitution influences the microbial metabolism. In consequence, it is believed to simulate more closely the physiology of a human gut.…”

The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

“…Given the diffi cult access to the mucosal environment, the development of gut simulators that accurately mimic mucosal microbial colonization is considered a strong asset to obtain a better understanding of the host-microbe interactome. It is in this philosophy that Van den Abbeele et al ( 2013 ) decided to optimize the SHIME for mimicking mucosal microbial colonization by incorporation of mucin-covered microcosms. The major fi nding of this so-called M-SHIME, or mucosal SHIME, was that colonization of the mucosal environment was characterized by a higher abundance of butyrate producing Clostridium clusters IV and XIVa.…”

“…While the overall colonization profi le was still representative of the in vivo colonization process, this slight bias has been a common observation for several dynamic models that work with luminal content only. Van den Abbeele et al ( 2013 ) succeeded in removing this colonization selectivity by incorporating mucin-covered microcosms in the SHIME, thereby creating the M-SHIME or mucosal SHIME. Butyrate producing Clostridium clusters IV and XIVa were found to specifi cally colonize the mucosal environment thereby compensating for their lower abundance in the lumen.…”

“…Specifi cally in the context of monitoring the initial stages of microbial colonization on the mucosal surface, 1-week experiments can be conducted. Distinguishing the mucosal from the luminal microbiome, Van den Abbeele et al ( 2013 ) evaluated the colonization process of the microbiome derived from fi ve human volunteers in M-SHIME systems over a timeframe of 5 days. The presence of mucins seems to play a specifi c role in the colonization process.…”

Prebiotics, Faecal Transplants and Microbial Network Units to Stimulate Biodiversity of the Human Gut Microbiome

“…Clostridium cluster IV and XIVa species (El Aidy et al, 2012b). The latter bacterial groups were previously reported to stimulate the expression of Tregs (Atarashi et al, 2011), potentially related to their strong capacity to colonize the mucin-associated microbiota (Van den Abbeele et al, 2012). Moreover, these Clostridium cluster IV and XIVa species represent only a small proportion of the microbial community in the inflammatory bowel disease patients (Frank et al, 2007).…”