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.


Study of skin microbiota in leprosy patients from India

Mycobacterium leprae (Wikipedia)

Leprosy is one among serious skin infection diseases present worldwide. Leprosy is associated with significant social stigma that renders the life of affected individuals difficult and isolated. Leprosy is caused by Mycobacterium leprae with a chronic granulomatous infection of the peripheral nerves along with the skin. The disease is characterized by damage of the peripheral nerves, mucous membranes, eyes and skin. Untreated skin especially on the face thickens because of dermal infiltration giving rise to the ‘leonine faces’. Skin is the primary organ affected in leprosy patients, though the role of skin microbiome in pathogenesis is not very well studied. One of the recent studies have shown that skin of leprosy patients harbors perturbed microbiota which grants inflammation and disease progression.

Researchers conducted a collaborative study in order to understand the lesional and non-lesional skin microbiota in leprosy patients. Different experimental techniques were used for conducting this study. DGGE is a molecular sequence dependent fingerprinting technique that allows characterization of the microbiota from large number of skin samples without pre-existing knowledge of its composition. In this study, nested PCR-DGGE and a comprehensive computational analysis for the microbial diversity exploration present in skin swab samples collected from LS and NLS sites was done. The overall objective of the study was to catalogue and compare the skin microbial communities present in healthy control with those in lesional skin (LS) and non-lesional skin (NLS) sites of Leprosy patients. According to the researchers, the results obtained from this study can potentially be used for generating preliminary hypotheses about interaction between disease causing microorganisms, microbial co-inhabitants and pathophysiology of the disease in leprosy patients.

A comprehensive analysis of 16S rRNA profiles was done, corresponding to skin samples from participants located in two geographical locations in India, Hyderabad and Miraj. Study participants were chosen from well-established leprosy research centers located in two geographically well-separated locations in India in order to understand if any variability occurs as a result of differences in food, climate and lifestyle. The genus Staphylococcus was one of the representative bacteria in healthy controls while it was underrepresented in skin microbiota of leprosy patients. Taxa affiliated to phyla Firmicutes and Proteobacteria were found in abundance in healthy controls and lesional skin, respectively.

While the NLS microbiota for LP from both Hyderabad and Miraj indicated the presence of similar microbiota with bacteria belonging to genus Canibacter, Corynebacterium, Cutibacterium, Janibacter, Moraxella and Staphylococcus, samples of LP from Miraj were observed to additionally harbour Bacillus, Methylobacterium, Microvirga, Paracoccus and Staphylococcus. Some of the important genera found in Hyderabad subjects were Canibacter, Corynebacterium, Cutibacterium, Janibacter, Moraxella and Staphylococcus while Miraj subjects had Bacillus, Methylobacterium, Microvirga, Paracoccus and Staphylococcus genera. Taxonomic analysis indicates presence of few taxa having distinct abundance trends between healthy control (HC) and leprosy patients (LP) : Acinetobacter, Corynebacterium, Kocuria, Micrococcus, Paracoccus, Propionibacterium, Staphlococcus were observed to be the most abundant common taxa in samples from both Hyderabad and Miraj.

Network analysis study reveals signature differences in microbial co-occurrence patterns in datasets corresponding to HC and LP. The skin lesions occurring on the lesional and non-lesional skin surface has analyzed some sort of abnormalities.  The abnormalities were structured to undergo through experimental sites that are lesional and non-lesional sites, and understand the severity of the disease.

Observed diversity level changes, shifts in core microbiota, and community network structure support the evident dysbiosis in normal skin microbiota due to leprosy. Insights obtained indicate the need for exploring skin microbiota modulation as a potential therapeutic option for leprosy.

In order to understand the detailed results in this study please refer: