Abstract
The present study compared bacterial and fungal diversity of kefir beverages produced using milk (MK) or sugared water (WK) as propagation matrices and grains from the cities of Curitiba (CU) or Salvador (SA), Brazil, by sequencing the complete set of RNA transcripts produced in four products. In Brazil, milk and sugared water are used as matrices to propagate kefir grains. In all beverages, the bacterial community was composed of Lactobacillaceae and Acetobacteraceae. Saccharomycetaceae was the yeast family more abundant in WK, and Dipodascaceae and Pichiaceae in MK. Regarding KEGG mapping of functional orthologs, the four kefir samples shared 70% of KO entries of yeast genes but only 36% of bacterial genes. Concerning main metabolic processes, the relative abundance of transcripts associated with metabolism (energy metabolism) and environmental information processing (membrane transport) had the highest water/milk kefir ratio observed in Firmicutes. In contrast, transcripts associated with genetic information processing (protein translation, folding, sorting, and degradation) oppositely had the lowest water/milk ratios. Concluding, milk and water kefir have quite different communities of microorganisms. Still, the main mapped functional processes are similar, with only quantitative variation in membrane transport and energy acquisition in the water kefir and protein synthesis and turnover in the milk kefir.
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Data availability
All data generated or analysed during the present study are available from the corresponding author upon request. The crude sequencing data were deposited at the US National Institutes of Health (NIH), National Library of Medicine (NLM), National Center for Biotechnological Information (NCBI), and Sequence Read Archive (SRA) database, accession number PRJNA1002349, Submission ID: SUB13729316, Release date: 2023–08-08.
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Acknowledgements
We acknowledge the CEPAD-ICB-UFMG for providing the Sagarana HPC Cluster as a computational resource.
Funding
The Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) supported this work (process 2070.01.0008851/2019–41; APQ 02928–16). The Pró-reitoria de Pesquisa da Universidade Federal de Minas Gerais (PRPq/UFMG), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Cooperation Project of Universidad Nacional de La Plata, Agencia Nacional de Promoción Científica y Tecnológica MINCYT (BR1301), and CAPES (245/14) also contributed with specific financial support.
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E.N. and A.C.N. designed and coordinated the study. J.R.N., G.R.F., A.G.A. and G.L.G. contributed with experimental support. D.L.R., P.C.L.S., C.S.S.M., A.A.B. and C.N.B.C.V. performed the kefir propagation, RNA extraction, libraries creation, metatranscriptomics sequencing and subsequent bioinformatics analyses. All authors read and approved the final manuscript.
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The project was approved by the competent authorities of the Federal University of Minas Gerais (UFMG) and Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) and carried out in strict accordance with scientific ethics, without harm to any person, animal, or the environment and its biodiversity.
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Rios, D.L., da Silva, P.C.L., Moura, C.S.S. et al. Comparative metatranscriptome analysis of Brazilian milk and water kefir beverages. Int Microbiol 27, 807–818 (2024). https://doi.org/10.1007/s10123-023-00431-4
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DOI: https://doi.org/10.1007/s10123-023-00431-4