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. 2022 Apr 10;59(10):3918–3927. doi: 10.1007/s13197-022-05421-4

Bacterial diversity of traditional fermented food, Idli by high thorough-put sequencing

Digambar Kavitake 1,#, Mangesh V Suryavanshi 2,3,#, Sujatha Kandasamy 1,#, Palanisamy Bruntha Devi 1, Yogesh Shouche 2, Prathapkumar Halady Shetty 1,✉
PMCID: PMC9525534  PMID: 36193360

Abstract

The bacterial composition of naturally fermented Indian food, Idli was studied by high-throughput Illumina amplicon sequencing at different taxonomic levels. Metagenomic investigation revealed fold change with respect to some of the phylotypes in 06th to 12th h of fermentation, suggesting the synergistic mode of nutrition. After 12th h fermentation, bacterial populations were stabilized towards 15th h fermentation. The bacterial phyla found as Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and others in various proportions with respective to fermentation time. Among these Firmicutes and Proteobacteria were the predominant bacterial associates in this product. Initially at 0th h time interval Firmicutes (7%) and Proteobacteria (93%) were present adequately in the product which has been changed to Firmicutes (68%), Proteobacteria (31%) at the end of the fermentation (15th h). Phylum Firmicutes represented various major genus such as Lactococcus, Weissella, Lactobacillus, Enterococcus, Bacillus and Macrococcus whereas Proteobacteria revealed the presence of Enterobacter, Erwinia, Serratia, Pseudoalteromonas, Vibrio and Klebsiella genus. Co-occurrence and Co-exclusion network were developed to ensure the positive and negative association in the eubacterial genus detected in entire batter fermentation event. Some genera like Weissella, Lactococcus and Enterococcus are showing increase in abundances in auxiliary succession events can be established for starter culture development.

Supplementary material

The online version contains supplementary material available at 10.1007/s13197-022-05421-4.

Keywords: Idli batter, Microbiome, Amplicon sequencing, Firmicutes, Proteobacteria

Introduction

Fermentation is one of the widely used traditional strategies for processing, preservation and to bring diversity to the food products. Distinct fermented foods from various regions are reported since many decades throughout the world. India is renowned for its ethnic diversity and biological resources, also recognized for amazing diverse food culture including ethnic fermented foods and beverages (Rao et al. 2005; Sekar and Mariappan 2007). Traditional foods are in habit for several years in India, although its preparation method varies within the country. Cereals and legumes are the forefront prime foods consumed by Indian population in diverse forms, including fermented foods. Although most of these traditional foods are homemade, few are commercially available in restaurants and industries as well (Das et al. 2012).

Idli is a popular cereal-legume based traditional fermented food widely consumed as a breakfast food in India (specially, Southern India) and Sri Lanka (Durgadevi and Shetty 2014). Idli consists of around 3.3 – 12% protein, 8.2 – 77.6% carbohydrate and 50.5% moisture (Ramalingam et al. 2019). It is a rich source of all essential amino acids required for daily diet which is attained by the co-fermentation of rice and black gram (Ray et al. 2016). The vitamins content of fermented idli batter are 0.59, 0.59, 0.76 mg/100 g of riboflavin, thiamine and folic acid respectively (Ghosh and Chattopadhyay 2011). Idli acts as a desirable dietary food for infants and invalids and nutritional supplement for children suffering from malnutrition and Kwashiorkor which increases the demand for this traditional product worldwide. In Idli preparation, fermentation plays an essential role in enriching the nutrition and protein efficiency value, high digestibility along with better texture and flavour of the final product (Nisha et al. 2005). The natural fermentation process involves a heterogeneous microbial community although mainly dominated by native lactic acid bacteria (LAB) and yeast that sequentially develop during the soaking process followed by the fermentation of Idli batter. In freshly fermented batter, LAB and yeast are in huge numbers varying from 109–1011 CFU/g (Iyer et al. 2013; Nisha et al. 2005; Sridevi et al. 2010). Each ingredient independently contributes to a diverse variety of indigenous LAB and yeast. Dynamics in microbial population during fermentation is also influenced by the alteration in temperature and climatic conditions. Several LAB such as Leuconostoc mesenteroides, L. lactis, Lactobacillus fermentum, L. plantaraum, L. coryneformis, L. delbrueckii, Streptococcus faecalis, Pediococcus cerevisiae, Weissella confusa and W. cibaria are identified from Idli batter (Soni et al. 1986; Saravanan et al. 2015). In addition, Bacillus subtilis, B. amyloliquefaciens, B. tequilensis B. polymyxa, Enterobacter sp. and Micrococcus varians are also reported. Likewise, yeast includes Saccharomyces cerevisiae, Hansenula anomala, Debaryomyces hansenii, Torulopsis candida and Trichosporon beigelii (Soni and Sandhu 1991). The majority of the earlier microbiological studies on Idli are based on regular isolation practices and conventional identification procedures which are prone to biases, low taxonomic community, misinterpretation of species and underestimation of species richness and diversity (Cocolin and Ercolini 2015). Application of high throughput metagenomic technologies possibly will provide more insights about the microbiota of the natural fermentation process. Studies on metagenomics of several fermented foods have exposed a realistic view of the microbial community structure and succession engaged in the natural fermentation. The present work was endeavoured to study the complete microbial community profile of traditionally prepared ethnic fermented food (Idli) at various stages of batter fermentation using targeted amplicon sequencing.

Materials and methods

Sample collection/sampling

Idli batter (IB) was prepared as per traditional protocol in our laboratory (Pondicherry University) in three sets with black gram and rice in the ratio of 1:4. Both were soaked separately in water for 4 h, and then black gram was ground finely whereas rice was ground coarsely using wet grinder (Singer Maxigrind Wet Grinder, India). Ground black gram and rice were mixed thoroughly in a 2 L capacity beaker and allowed to ferment for up to 15 h under ambient conditions (30 ± 2 °C). Batter samples were collected at different fermentation time intervals (0 h representing the just ground and mixed batter, 6, 12 and 15 h representing various stages of fermentation) and stored at -20 ºC until further analysis with codes IB-0, IB-06, IB-12 and IB-15.

Metagenomic DNA extraction

Total genomic DNA extraction was performed using conventional method with slight modifications (Gaikwad 2002). Briefly, 1 g of Idli batter was suspended in 1 mL of STE (Sodium Chloride-Tris–EDTA) I buffer (100 mM NaCl, 10 mM Tris HCl (pH 8), 1 mM EDTA), centrifuged at 10,000 × g for 2 min and the pellet was resuspended in 500 µL of STE II buffer (100 mM NaCl, 10 mM Tris HCl (pH 8), 25 mM EDTA). Then, 100 µL of 5% SDS were added, mixed well and heated at 70 °C, 20 min. The tubes were cooled to room temperature and mixed with an equal volume of chloroform (600 µl) and 100 µl of buffer saturated phenol. The tubes were vortexed, centrifuged again at 10,000 × g for 10 min and the aqueous phase was transferred to fresh tubes with 200 µl TE (Tris–EDTA) buffer. Next, equal volume of chloroform and isoamyl alcohol was added, vortexed and the aqueous phase was again transferred to fresh tubes. To the aqueous phase, 1/10th volume of 3 M sodium acetate (pH 7.0) and 0.6 volume of isopropanol was added and left overnight at 4 °C. The precipitate after centrifugation at 1000 × g for 15 min were washed with 70% ethanol and suspended in 50 µl TE buffer. DNA was separated in 1% agarose gel electrophoresis and visualized with a UV transilluminator (MEDOX-BIO UV Transilluminator – Regular, MX-1208–01) after staining with 0.5 g/ml of ethidium bromide.

16S rRNA gene sequencing and downstream analysis

Microbial communal structure was studied using 16S rRNA amplicon sequencing at each time interval in order to reveal the composition of bacterial species. Briefly, the V3 region of 16S rRNA gene was amplified with hi-fidelity AmpliTaq gold master mix (Invitrogen Inc., USA) and bacterial universal primers (341 F 5′-CCTACGGGAGGCAGCAG-3′ and 518 R 5′-ATTACCGCGGCTGCTGG-3′) (Bartram et al. 2011). PCR amplification, PCR products purification, amplicons assessment and sequencing on Ion Torrent Personal Genome Machine (Life Technologies, USA) for 130 cycles were performed as per the method described earlier by Bhute et al. (2016). Similarly, total 358,724 raw reads were obtained from PGM machine, and pre-processing were done using Mothur pipeline (Schloss et al. 2009) with following conditions: (1) minimum length–150 bp, (2) maximum length–200 bp, (3) maximum homopolymer–5, (4) maximum ambiguity–0, and (5) average quality score–20. So far total of 165,154 high-quality amplicon reads (min-3132, max- 20,439 reads per sample) were obtained after pre-processing. These high-quality amplicon reads were pooled in single fasta file and imported to the QIIME (Quantitative Insights Into Microbial Ecology) v.1.9 (Caporaso et al. 2010) for the further analysis. We performed the Operational Taxonomic Units (OTUs) picking at 97% sequence similarity using UCLUST algorithm, and align representative sequences against Greengenes 13.8 database to obtain reference based OTUs to each sequence. Subsequently, all reads were assigned to the lowest possible taxonomic rank by utilizing RDP Classifier 2.2 with a confidence score of 80%. All unaligned and chimeric sequences were excluded from alignment and downstream analysis.

Data availability

Sequencing data have been deposited to NCBI Sequence Read Archive under accession number: SRP174635 and BioProject ID: PRJNA511947.

Statistical analysis

Alpha diversity was expressed by using the Chao1 index, Good’s coverage, Shannon and Simpson index. The Shannon index, Chao 1 index represent species richness in samples. The Simpson index is used to measure the degree of concentration of species; where 0 represents infinite diversity as well as 1 represents no diversity.

Results

The alpha diversity in Idli samples

After sequencing, generated dataset of 358,724 raw sequences was filtered to achieve 216,931 high quality sequences. Sequences usable to QIIME reference database for OTU picking were measured as 165,154. Derived OTU table has been subjected to remove the cyanobacteria and chloroplast hits and we got total 1298 OTUs from the sequence analysis. Those OTU table has been used for the further diversity assessments. The microbial alpha diversity, including Chao1 index, Good’s coverage, Shannon index, and Simpson index was estimated using the QIIME platform (Table 1).

Table 1.

Alpha diversity indices for the batter fermentation

Fermentation time (h) Chao 1 index Good’s coverage Shannon Simpson index
0 (n = 3) 545.371 0.984781 5.721107 0.94471
6 (n = 3) 605.274 0.990774 4.462373 0.84020
12 (n = 3) 731.861 0.978004 5.012041 0.87751
15 (n = 3) 772.467 0.989357 4.305185 0.80900
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Bacterial community profile of Idli

The bacterial composition of naturally fermented Indian food Idli, was studied at different taxonomic levels. Phylogenetic tree revealed the taxonomic affiliations to all observed OTUs (Operational Taxonomic Units) in entire sampling sets. Taxonomic positions were derived from the gg_13.8 database taxonomy (Fig. 1). The bacterial phyla present in this product were Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and others in various proportions with respect to fermentation intervals (Fig. 2). Initially at 0th h, the batter was inhabited with lower population of Firmicutes (3%) and higher Proteobacteria (97%), which has been reversed with higher Firmicutes (68%) and lower Proteobacteria (31%) at the end of the fermentation (15th h). Phylum Firmicutes represented various major families like Bacillaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae which consists the foremost genus such as Lactococcus, Weissella, Pediococcus, Lactobacillus, Enterococcus, Bacillus and Macrococcus whereas Proteobacteria revealed the presence of Enterobacteriaceae, Moraxellaceae, Pseudomonadaceae and Vibrionaceae families consisting Enterobacter, Erwinia, Serritia, Pseudoalteromonas, Vibrio and Klebsiella as a major genus (Fig. 2). Meanwhile, 1% Bacteroidetes were observed at 06th and 12th h intervals along with trace amount of Actinobacteria species.

Fig. 1.

Fig. 1

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Phylogenic Tree showing the taxonomic affiliations to all observed OTUs (Operational Taxonomic Units) in entire sampling sets. Taxonomic positions were derived from the gg_13.8 database taxonomy and unclassified OTUs were omitted during the tree construction

Fig. 2.

Fig. 2

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(a) Families and their respective phylum level distribution of bacterial communities of Idli at different time interval of fermentation. (b) Genus level distribution of bacterial communities of Idli at different time interval of fermentation

Co-occurrence and Co-exclusion network described the positive and negative association in the eubacterial genus detected in entire batter fermentation event. Spearman correlation significant values (p =  < 0.05) on OTUs level matrix were used to show the positive association (red color bridge) and negative association (blue color bridge) for each genus (Fig. 3). Number of species phylotypes under the different family level taxonomy was observed in batter fermentation at various time intervals. Bacterial dynamics of Idli batter is clearly visible in Fig. 4. As fermentation time passed especially after 12 h, the microbial diversity was increased gradually.

Fig. 3.

Fig. 3

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Co-occurrence and Co-exclusion network describing the positive and negative association in the eubacterial genus detected in entire batter fermentation event. Spearman correlation significant values (p =  < 0.05) on OTUs level matrix were used to show the positive association (red color bridge) and negative association (blue color bridge) for each genus

Fig. 4.

Fig. 4

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Number of species phylotypes under the different family level taxonomy was observed in batter fermentation at various time intervals

Differences in microbiota among Idli at various time intervals

There are 35 number of core genus was observed in total sample population (Supplementary file 1). Interestingly, as fermentation time increases, we observed shift in the bacterial flora includes 23 number was depleted and 12 numbers was newly observed after the 12 h fermentation. Some of core genera were found to dwell significantly with the fermentation time. Log transformed values of abundance mean of each core genus (represented in 90% of samples) were taken for the fold change analysis. Core genus with fold change values for before and after 12th h fermentation time were depicted in the form of bar diagram (Fig. 5). Micrococcus, Bacillus, Chryseobacterium, Exiguobacterium, Staphylococcus, Achromobacter, Acinetobacter, Citrobacter, Enterobacter, Enhydrobacter, Erwina, Ferrimonas, Klebsiella, Paracoccus, Plesiomonas, Pseudoalteromonas, Serratia, Stenotrophomonas, Vibrio and Xenorhabdus were observed in initial 12 h interval whereas Sphingobacterium, Corynebacterium, Wautersiella, Clostridium, Enterococcus, Lactococcus, Lysinibacillus, Paenibacillus, Comamonas, Pseudomonas and Shewanella were observed after 12 h.

Fig. 5.

Fig. 5

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Core genus with fold change values for before and after 12th hr fermentation time

Discussion

The aim of this study was to explore the bacterial community composition of Idli batter at various time intervals during the fermentation process. The results showed that Idli is composed various phyla like Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria and Bacteroidetes, among which Firmicutes and Proteobacteria are predominantly present throughout the batter fermentation. At the end of the fermentation Firmicutes presences was adequately increased (70%) compared to initial one (7%) whereas Proteobacteria was decreased over the time (from 93 to 29%). At initial stages Proteobacteria was dominating the batter fermentation process, which decreased at the end of fermentation due to the production of organic acids (specially, lactic acid) by lactic acid bacteria from Firmicutes group; resulting in domination of Firmicutes at the end.

As per the traditional approach for making Idli, batter fermentation has to happen for 12–14 h (slightly variable based upon quality and ratio of ingredients). After 15th h over-fermentation takes place, where excess microbial growth occurs which resulting in high acidity and degradation/conversion of nutrients. And, over fermentation affects the quality parameters of Idli, such as texture, sensory and nutritional characteristics. In the Idli fermentation, pre-soaking of rice and black gram dhal prior to the grinding is an important step in the fermentation (Desikachar et al. 1960). In this study, we have soaked, grinded and fermented samples till 15th h and microbiome have been analysed at every 0, 6, 12 and 15th h time interval. In earlier report on Idli, Mandhania et al. (2019) reported the microbiome of Idli samples collected from three different places Bangalore, Pune and laboratory prepared one. In agreement with earlier report, we also found the similar trend of microbiome in fermentation process and, additionally, observed the structural diversity change throughout the fermentation which is about increasing in Firmicutes and decrease of Proteobacteria taxon when fermentation time has been increased. Moreover, Mandhania et al. (2019) reported the changes in the Firmicutes and Proteobacteria abundance were observed for these samples from different geographies like: Bangalore (60.3%, 36.1%), Pune (32.8%, 54.7%) and laboratory prepared batter (65.5%, 28.6%). Our samples reporting from Pondicherry showed the highest (68.42%) abundance of Firmicutes compared rest of all. These variations occurred, majorly due to the difference in geographical locations as well as quality differences in raw ingredients, difference in dhal and rice ratio for making batter, and different fermentation time.

The phylum Firmicutes majorly revealed the presence of Leuconostocaceae, Enterococcaceae, Streptococcaceae and Bacillaceae families (Fig. 2) with the genera as Weissella, Lactococcus, Lactobacillus, Enterococcus, Bacillus and Macrococcus. Similar genera have been reported by Saravanan et al. (2015) from Idli batter. Abundance and potential key role (Mandhania et al. 2019) and probiotic potential (Sharma et al. 2018) of Weissella in Idli have been reported earlier. These genera are known to retain numerous constructive properties leading towards upright health benefits by means of diverse mechanisms (Fijan 2014; Marco et al. 2017; Wedajo 2015).

Many Firmicutes from Idli batter are very well known for the production of exopolysaccharides (EPS) such as glucan (Saravanan et al. 2019), galactan (Kavitake et al. 2016) and dextran (Sawale and Lele 2010). Last few decades, EPS producing several strains of Weissella genus (Firmicutes) are identified and under study for their functional properties and applications which having prominent techno-functional and biological potentials and hence contributes crucial role in improving nutritional and functional status of the fermented foods. Also, some Firmicutes from Idli batter like Enterococcus (Vijayendra et al. 2010), Pediococcus (Sadishkumar and Jeevaratnam 2018) and Lactobacillus (Borase et al. 2015; Mehra and Chopra 2015) are known to produce bacteriocins which inhibit the growth of pathogens. The antimicrobial properties of bacteriocin against closely correlated bacteria and other non-relative bacteria to promote its own growth and avoid the food spoilage became a trademark approach in food fermentation and preservation to achieve food safety.

Fermentation process leads to the breakdown of the raw material and production of organic acids, mainly lactic acid and results to rapid acidification. In addition to organic acids, certain volatile, aromatic compounds, bacteriocins, enzymes and several EPS are also produced. Genera from Firmicutes are acid tolerant hence can be a good candidate in the starter culture development for Idli batter. With the same perspective, earlier Enterococcus, Pediococcus and Weissella are recommended for the starter culture development (Sridevi et al. 2010; Mandhania et al. 2019) which can enhance the shelf life, aroma, taste, texture, nutritional and functional value of the food (Steinkraus 2002). This study provides in-depth information on Idli microflora at various stages of fermentation. Firmicutes have dominated the later stages of fermentation which has the potential to play a significant role in the control fermentation and aroma generation. Lactic acid, bacteriocins and EPS producing candidates from Firmicutes can be the potential starter culture for good quality of Idli.

Conclusion

The bacterial diversity of Indian fermented food (Idli) was studied at different taxonomic levels by high-throughput Illumina amplicon sequencing. Different phylum dynamics was observed in various proportions with respective to fermentation time, majorly including Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria and Bacteroidetes. Initial fermentation was dominated by Proteobacteria (93%), however at the end of the 15th h Firmicutes (68%) have dominated the fermentation. Both the phylum Firmicutes and Proteobacteria represented major genus such as Lactococcus, Weissella, Lactobacillus, Enterococcus, Bacillus, Macrococcus, Enterobacter, Erwinia, Serratia, Pseudoalteromonas, Vibrio and Klebsiella. These results hava a significant role in the development of functional starter culture for Idli fermentation based upon the revealed bacterial dynamics.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (XLSX 19 KB) (18.9KB, xlsx)

Acknowledgements

We acknowledge Department of Food Science and Technology, Pondicherry University, Pondicherry and National Centre for Microbial Resource, National Centre for Cell Science, Pune for providing support and requirements to this study. DK and PBD are thankful to University Grants Commission, New Delhi for Senior Research Fellowship (1532/OBC-PWD/NET-DEC.2015) and Kothari Post-Doctoral Fellowship (201920-BL/19-20/0192) funding.

Authors contribution

DK, SK, PHS, MVS and YS contributed in planning and designing of this research framework. SK and DK collected the samples and performed DNA isolation experiments. MVS and YS has processed 16S rRNA amplicons sequencing and performed detailed bioinformatics analysis. DK, MVS, SK, PBD, YS and PHS analyzed, drafted and corrected the data for manuscript. All authors read and approved the final manuscript.

Funding

Not applicable.

Data availability

Sequencing data have been deposited to NCBI Sequence Read Archive under accession number: SRP174635 and BioProject ID: PRJNA511947.

Declarations

Conflict of interest

Authors do not have any kind of conflict of interest.

Ethics approval

Authors are assuring that the work is original and has not been published elsewhere; either completely or in partial format and the manuscript has not been submitted to any other journal. The present study did not include any animal or human studies.

Consent to participate

Not applicable, no human subjects were involved in this study.

Consent for publication

Not applicable.

Footnotes

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Digambar Kavitake, Mangesh V. Suryavanshi and Sujatha Kandasamy the authors are have contributed equally.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary file1 (XLSX 19 KB) (18.9KB, xlsx)

Data Availability Statement

Sequencing data have been deposited to NCBI Sequence Read Archive under accession number: SRP174635 and BioProject ID: PRJNA511947.

Sequencing data have been deposited to NCBI Sequence Read Archive under accession number: SRP174635 and BioProject ID: PRJNA511947.

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