Molecular characterization of microbial communities and development of starter culture from traditionally fermented milk, amabere amaruranu in Kisii County, Kenya

Abstract

Spontaneously fermented milks are integral to human diets in many African communities, These products have found their way into the informal market posing a public health concern because their quality and safety is not ascertained. Consequently, there is need to isolate and identify microbial strains with superior fermentative qualities and attributes of health qualities as starter cultures to commercialize production as well as profile potential microbial hazards. The aim of this study was to characterize microorganisms in amabere amaruranu for identification of starter cultures for the fermentation of milk under controlled fermentation conditions to improve quality and safety. Forty-six (46) samples of amabere amaruranu were collected from Kisii County and characterized for total viable counts (TVC), total coliform counts (TCC), lactic acid bacteria (LAB) and yeasts and moulds using cultural methods. To isolate LAB as potential starter cultures, discrete colonies on MRS agar were selected and purified by repetitive streaking on de Man, Rogosa and Sharpe (MRS) agar. Thirty-seven (37) colonies were selected for phenotypic (Gram staining and catalase test) and physiological characterization DNA of the isolates was extracted for identification by 16S rRNA gene sequencing. The obtained sequences were compared to DNA sequences in the GenBank by the BLASTN Program and aligned in Mega 6.0. Fermentation capability was assessed by lactic acid production and pH change. The bacterial counts were 3.82- 10.98 log 10 cfu/ml (TVC), 3.52–9.01 log10 cfu/ml (TCC), and 3.52–11.32 log10 cfu/ml (LAB), while the yeasts and moulds were 0.00–9.05 log10 cfu/ml. Five species of lactic acid isolates were identified by sequencing of which Lactobacillus plantarum was the most predominant species. Lactobacillus plantarum had good acid production capability within 16 hours. These results show that, it is possible to characterise microbial diversity of amebere amaruranu using both cultural and molecular techniques. Amabere amaruranu contains diverse microbial populations in terms of type and numbers. Lactobacillus plantarum in amabere is a potential starter culture that could be used to upgrade production of fermented milk. Lactobacillus planturum has good fermentation capabilities hence could be used as starter culture for product development.