Study of probiotic potentials of microbial communities associated with fermented foods of northeast India

Probiotics are described as “Live microorganisms which when administered in adequate amounts confer a health benefit on the host”. Probiotics are commonly consumed functional food. Probiotics are reported to improve the immunological and gastrointestinal functions, it also plays role in reducing the risk of cancer and cardiovascular diseases.

Ethnic fermented foods have been consumed since ancient times with the notion that they provide health advantages and could be a source of probiotics. We know very little about microorganisms involved in the fermentation process of these foods. A study was conducted by team of Dr. Avinash Sharma at NCMR-NCCS Pune to understand the microbial community associated with the ethnic fermented food from northeast part of India, using high throughput sequencing approach. Three ethnic fermented foods were chosen as samples: ‘Axone’, ‘Bastenga’ and ‘Chathur’. Food specific enrichment of bacterial genera was observed as Lactobacillus (90.7%) in ‘Axone’, Bacillus (62%) and Clostridium (15.9%) in ‘Bastenga’ and, Lactobacillus (47.8%) and Staphylococcus (36.3%) in ‘Chathur’, whereas Saccharomyces (98.7%) belonging to phylum Ascomycota predominates the fungal communities among all the samples.

Three different ethnic fermented food preparations were sampled in triplicates from a local household in Manipur and Nagaland, states of North East India. The ‘Axone’ or ‘Glycine max’, a preparation made of fermented Soybean and the ‘Bastenga’, a fermented bamboo shoot were collected from Dimapur, Nagaland, whereas ‘Chathur’ a locally brewed beer out of fermented rice was collected from Ukhrul, Manipur. Amplicon sequencing approach was employed by targeting V4 region of 16S rRNA and ITS gene to identify the consortia of bacteria, yeasts and molds. Further, the research team screened the probiotic potential of microbial communities associated with these food preparations by using approach of metagenomic imputation followed by mapping against set of known genes catering probiotic properties.

Bacterial diversity study revealed that ‘Axone’ have least diversity of microbes while ‘Chathur’ represents most diverse sample. Assessment of fungal communities indicated ‘Chathur’ being highly diverse while ‘Bastenga’ representing least diverse sample. Investigation of bacterial community composition revealed predominance of bacterial phylum Firmicutes followed by Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Fusobacteria accounting for 99.9% of bacterial communities. The samples Axone and Bastenga contain Firmicutes as the main phylum with relative abundance of 98.4% and 99.2%, respectively. In contrast, Chathur comprises of Firmicutes (81.1%) and Proteobacteria (10.1%) as the most abundant phyla.

Interestingly, Lactobacillaceae dominates in Axone , whereas Chathur harbors Lactobacillaceae , Clostridiaceae and Bacillaceae as the major constituents. Further, Bastenga comprised of Bacillaceae and Staphylococcaceae. Likewise, at genera level Lactobacillus out numbers other bacterial members for the Axone. Genera Lactobacillus and Bacillus were found to dominate in case of Chathur and Bastenga , respectively. Additionally, Chathur consists of Clostridium, Bacillus ,Pediococcus, Streptococcus, Geobacillus, Staphylococcus, Weissella whereas Bastenga comprises of Staphylococcus being the second most prevalent taxa.

The use of high throughput sequencing to investigate ethnic fermented foods gives key info on microbial community structure, especially major contributors associated to fermentation processes. The findings of this work indicate that integrating culture-dependent techniques and comparative genomics, it may be possible to identify indigenous probiotic candidates.


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