Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community; Kefir fermentation curve (FIA-MS)

ABSTRACT:

Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realises stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.

Linked metabolomics studies:

MTBLS1823 Spent-medium assay, measured untargeted (FIA-qTOF) and targeted (HILIC, LC-MS)

MTBLS1830 Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)

Linked cross omic data sets:

Genomes of isolated kefir species are available in the NCBI database under the accession: PRJNA375758 (bioproject ID: 375758).

Metatranscriptomic sequencing data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB37001.

Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.

INSTRUMENT(S): Flow injection analysis MS - negative

SUBMITTER: Eleni Kafkia  Sonja Blasche  Ruben Mars 

PROVIDER: MTBLS1829 | MetaboLights | 2020-11-04

REPOSITORIES: MetaboLights