Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use

ABSTRACT

Diverse intestinal microbiota is frequently used in in vitro bioreactor models to study the effects of diet, chemical contaminations, or medication. However, the reproducible cultivation of fecal microbiota is challenging and the resultant communities behave highly dynamic. To approach the issue of reproducibility in in vitro models, we established an intestinal microbiota model community of reduced complexity, SIHUMIx, as a valuable model for in vitro use.

The development of the SIHUMIx community was monitored over time with methods covering the cellular and the molecular level. We used microbial flow cytometry, intact protein profiling and terminal restriction fragment length polymorphism analysis to assess community structure. In parallel, we analyzed the functional level by targeted analysis of short-chain fatty acids and untargeted metabolomics. The stability properties constancy, resistance, and resilience were approached both on the structural and functional level of the community. We show that the SIHUMIx community is highly reproducible and constant since day 5 of cultivation. Furthermore, SIHUMIx has the ability to resist and recover from a pulsed perturbation, with changes in community structure recovered earlier than functional changes.

Since community structure and function changed divergently, both levels need to be monitored at the same time to gain a full overview of the community development. All five methods are highly suitable to follow the community dynamics of SIHUMIx and indicated stability on day five. This makes SIHUMIx a suitable in vitro model to investigate the effects of e.g. medical, chemical, or dietary interventions.

KEYWORDS:

• Bioreactor
• flow cytometry
• protein profiling
• metabolomics
• t-RFLP
• short chain fatty acids
• intestinal microbiota
• in vitro model
• simplified human intestinal microbiota (SIHUMI)

Acknowledgments

We thank the German Federal Environmental Foundation (DBU) for financial support of Jannike Lea Krause. We thank Prof. Dr. Michael Blaut (German Institute of Human Nutrition, Potsdam-Rehbruecke) for providing the SIHUMIx bacteria. We are thankful for technical assistance from Jeremy Knespel, Eva-Annamaria Stier, Kathleen Eismann and Nicole Gröger and for culture medium supply from Martina Kolbe.

Authors’ contributions

JLK (Jannike Lea Krause) and SSS (Stephanie Serena Schaepe) performed the bioreactor experiments and evaluated the data. KFW (Katarina Fritz-Wallace), BE (Beatrice Engelmann) performed the metabolome analyses and were supported by URK (Ulrike Rolle-Kampczyk). JLK, FS (Florian Schattenberg) and ZL (Zishu Liu) performed the flow cytometric analyses with support from SM (Susann Mueller). JLK, did the t-RFLP analyses supported by SK (Sabine Kleinsteuber). SSS did metproteomics with support from NJ (Nico Jehmlich). MvB (Martin von Bergen) and GH (Gunda Herberth) conceptualized the study. All authors contributed to and approved the manuscript.

Availability of data and materials

Raw cytometric data can be found at flow repository ID: FR-FCM-ZYVG under: https://flowrepository.org.

Disclosure of potential conflicts of interest

The authors report no conflict of interest.

Supplemental material

Supplemental data for this article can be accessed on the publisher’s website.

Additional information

Funding

Stephanie Schäpe is grateful for support from a DFG-grant within the Priority Program [1656], and Martin von Bergen acknowledges partial funding by DFG Priority Program [1382].