Molecular characterization of Bacillus , lactic acid bacteria and yeast as potential probiotic isolated from fermented food

Spontaneous fermentation or traditional method of preserving indigenous foods using sev- eral microorganisms, is frequently practiced in the marginal world. Fermented seeds and milk are mostly consumed in the form of food condiments and desserts in Africa, Asia and others parts of world. Our previous studies deal with the production of Bacteriocin-Like Inhibitory Substances by Bacillus from fermented food and quality of fermented milk consumed in Burkina Faso. The rep-PCR and sequencing were used to characterize thirty eights strains isolated various fermented foods from Burkina Faso. Phylogenetic tree were constructed by the neighbour-joining method based on 16S or 26S rRNA genes sequences using MEGA X. Based on colonies characteristics and cells morphology, biochemical tests and gene sequencing, the isolates were identiﬁed as Bacillus cereus sensu lato (13), Bacillus pumilus group (03) with one strain (LCG1) presumed LAB was identiﬁed as Bacillus australimaris or Bacillus pumilus by 16S rRNA sequencing, Enterococcus durans (03), Lactobacillus paracasei (03), Lactobacillus plantarum (04), Leuconostoc pseudomesenteroides (01), Saccharomyces cerevisiae (04), Kluyveromyces marxianus (01), Candida tropicalis (01), Pichia kudriavzevii (01), Clavispora lusitaniae (02), Rhodotorula mucilaginosa (01) and, Cyberlind- nera fabianii (01). Several microorganisms with potential technological interest are housed in fermented foods from Burkina Faso. These microorganisms are responsible for the fer- mentation of food through their enzymatic activity, leading to production of fermented food with desirable organoleptic characteristics, improved food safety, the enrichment of nutrients and the promotion of health of consumers. at species level by sequencing rRNA. As for several i.e. colonies varying not ovoid, and (1 were observed. These isolates were as Bacillus , and yeasts according to their and biochemical according or 26S rRNA sequencing was performed for the molecular identiﬁcation of isolates. Our ﬁndings conﬁrmed that the rep-PCR and 16S or 26S rRNA analysis provides good based on seed, roots and fermented milk of animals from Burkina Faso was conﬁrmed to be rich in Bacillus , LAB and yeast. B. pumilus, B. cereus, Enterococcus durans, Lactobacillus paracasei, Lactobacillus plantarum, Leuconostoc pseudomesenteroides, Saccharomyces cerevisiae and Kluyveromyces marxianus are the most studied strains and used as probiotics . These microorganisms are involved in both spontaneous fermentations and large-scale fermentation processes for the preservation and transformation of many raw food materials. Their metabolites may contribute to characteristics these fermented foods. Thus, the fermented milk and seeds are important sources of foods contributing to resolve the problems of diseases in world developing countries.


Introduction
Fermentation is an old method used by the nomadic peoples of sahelian countries for the processing and preservation of milk and other food products. This fermentation vary considerably among regions in South East Asia to Africa, ethnics and cultural knowledge [1] . Fermented foods have been used since Pharaonic Egypt to identify the diets and many tribes in the world. Thus, theses fermented foods have a long history in the developing world, particularly in Burkina Faso. Several fermented foods and beverages like fermented condiments ( Bikalga, Maarri, Soumbala ), fermented milk (traditional yogurt), fermented cereal ( Dolo , Porridges), fermented fruit products, fermented roots products ( Attiéké) and others are produced and consumed daily in many rural zones in Burkina Faso. Thus, the characteristics of these foods are due to a microbial diversity including namely bacteria, yeasts and moulds, which originate from the raw materials or often inoculated by starters [2] .
Several studies already carried out showed the composition and the importance of Attiéké, Bikalga , fermented milk, Maarri and Soumbala in the human consumption to resolve the major health issues of malnutrition [3 , 4] . The organoleptic and sanitary qualities of these products are due to the consortium of microorganisms including as well lactic acid bacteria (LAB), Bacillus , yeasts and moulds, which, by their metabolites, give a diversity of products finished after fermentation highly appreciated by the consumers [5] . These fermented foods have been used empirically in the past in medicine, but currently their properties for medical purposes have been confirmed by scientific studies [6] . Lactobacilli and Akkermansia are the most bacteria used as "probiotic ". Nowadays, LAB are the microorganisms the most studied and used in the agro-alimentary, pharmaceutical and cosmetic industries [7] . The microbiota of spontaneous fermentation of the food matrices origin African is dominated by a consortium of microorganisms including Bacillus , LAB and yeasts.
Several potential probiotic are hosted in fermented foods and used in areas of life [8] . In the process of selection of the starters, one of the first stages is the identification of strain, followed to evaluate the technological aptitudes, the harmlessness of the strain and its stability. This identification has recourse to the techniques of molecular biology, because the traditional bacterial farming techniques are not enough to study the complex microbial populations. These tools have largely contributed to identification, classification and reclassification of certain bacterial groups by molecular methods as sequencing, ribotyping, Amplified Fragment Length Polymorphism and rep-PCR [9] . Rep-PCR is a potential tool that uses different primers (REP, ERIC, NGREP, BOX, DRREP, MBOREP, GTG 5 ) set to analyse the phylogenetic relationship and also to know the genetic variability between the strains [10] . Initial genotyping concentrated on developing assays to differentiate microbial populations. This is a progression from phenotypic characterisation of isolates and afforded more robust methods for monitoring microbial strains of interest or investigating the diversity and dynamics of the cultivable component beyond species level. In general, such genetic fingerprinting provides subspecies discrimination, although certain assays also enable species identification. Thus, several sequences of rRNA or rDNA genes are available to scientists and researchers on Internet network, in general databases as GenBank ( http://www.ncbi.nlm.nih.gov/ ), ABIS online for bacterial identification ( http://www.tgw1916.net/bacteria _ logare _ desktop.html ), specialized databases as ribosomal project ( http://rdp.cme.msu.edu/ ), European ribosomal RNA ( http://www.psb.ugent.be/rRNA/index.html/ ), and EZbiocloud (https://www.ezbiocloud.net/) which is a database containing only the sequences of ARN 16S references strains, and the YeastIP databases ( http://genome.jouy.inra.fr/yeastip/ ). In this work, the objectives were to group and to identify the strains respectively by rep-PCR fingerprinting and the sequencing of the rRNA 16S bacteria and rRNA 26S yeasts isolated from fermented indigenous food of Burkina Faso, as well as their diversity to the research of new starters as potential probiotic.

Sampling
Sampling were realized in six (06) cities of Burkina Faso. Fermented condiments and food samples were purchased in markets from Ouagadougou. Fermented milk samples were purchased in markets from Bobo-Dioulasso, Djibo, Dori, Gorom-Gorom and Sebba . This choice of cities was justified by in fact that Ouagadougou is a commercial center, while the others cities are the major centers of milk production in Burkina Faso. The samples were transported to the laboratory at 4-5 °C using icebox for the different analysis.

Isolation and conservation
Bacillus were isolated in our precedent study and conserved at + 4 °C in Brain Heart Infusion with 15% (v/v) glycerol after 24 h incubation at 37 °C [11] . LAB were isolated on Man Rogosa Sharp agar (MRS) added the Nystatin (100 mg/L) and conserved in MRS broth with 30% (v/v) glycerol at −20 °C. Yeasts were isolated on Sabouraud CAF agar with chloramphenicol and conserved at + 4 °C in nutrient broth with 15% (v/v) glycerol.

Characterization of isolates
Purified microorganisms were grown for 48 h on appropriate media at 37 °C for bacteria and at 30 °C for yeasts then characterized. Cell morphology, Gram stain (only bacteria), catalase test, oxidase reaction, spore forming and cell motility were determined for all isolates.

Molecular analysis
A total of thirty eight isolates including fifteen Bacillus, twelve LAB and eleven yeasts, representing different groups according to morphological, biochemical characteristics were chosen for molecular typing.

DNA extraction
Each isolate was streaked on the appropriate agar and incubated at 30 °C for 48 h under anaerobic conditions (Anaero-Gen) for LAB and aerobic conditions for Bacillus and yeasts. The InstaGene Matrix Kit (Biorad 732-6030, Hemel Hempstead UK) was used for the DNA extraction according to the manufacturer's instructions. DNA purity was verified via a spectrophotometer after extraction and stored at −20 °C according to Ouoba et al. [12] .

Repetitive sequence-based PCR
Bacillus , LAB and yeasts were differentiated by rep-PCR (repetitive sequence based polymerase chain reaction). The rDNA of selected strains was amplified by PCR procedure described by Ouoba et al. [12] using the GTG 5 (5 -GTGGTGGTGGTGGTG-3 ). DNA molecular marker (12,0 0 0 pb, Promega, USA) was included as a standard. The migration of the gel was carried out in water during 16 h and 30 min at 47 V in 1X TAE (Tris, Acetate EDTA buffer) and photographed using an UV transilluminator. The strains were clustered according to their DNA profiles obtained.

Sequencing of 16S rDNA of bacteria and 26S rDNA of yeasts
One representing of each group were selected for sequencing. All PCR products were purified using kit GFX TM PCR DNA and Gel Band Purification Kit (GE Healthcare) and sequenced by Source Bioscience Sequencing (Cambridge, UK). For the bacteria ( Bacillus and LAB), the 16S rDNA were sequenced as described by Ouoba et al. [12] . A 540 bp portion of conserved regions of 16S rRNA gene was amplified using primers pA (5 -AGAGTTTGATCCTGGCTCAG-3 ) and pE (5 -CCGTCAATTCCTTTGAGTTT-3 ) and sequenced with primer pD (5 -GTATTACCGCGG CTGCTG-3 ) corresponding the position 536-518 bp of 16S rRNA gene of the E. coli . Yeasts were identified by sequencing of 26S rDNA to D1/D2 region. NL1 (5 -GCATATCAATAAGCG GAGGAAAAG-3 ) and NL4 (5 -GGTCCGTGTTTCAAGACG G-3 ) were used for amplification and sequencing [13] . All primers of sequencing genering approximatively 550 bp.

Identification of isolates
The search in database of 16S or 26S rRNA genes sequences was performed in GenBank NCBI ( http://www.ncbi.nlm. nih.gov/ ) using the BLAST program, a base of given general practitioner. A second database search for 16S rRNA gene sequences was performed using EZbiocloud ( https://www.ezbiocloud.net/ ) server, which is a database containing only 16S rRNA sequences of references bacteria. The YeastIP is a database ( http://genome.jouy.inra.fr/yeastip/ ) for 26 rRNA sequences of references yeasts according to Weiss et al. [14] .

Phylogenetic trees realization
The alignment of the obtained sequences was checked manually and corrected, and similarity values were determined by Chromas software (version 2.6.5). MEGA X was also used for alignment (Muscle algorithm) and to construct a consensus Neighbour-Joining analysis to assess the phylogenetic relationship of species of the Fusobacterium gastrosuis (LN906797). Gaps were excluded. The robustness of tree branches was assessed with 10 0 0 replicates. Phylogenetic and molecular evolutionary analyses were conducted according to Felsenstein [15] , Tamura and Nei [16] and Kumar et al. [17] .

Sequence accession numbers
The sequences determined in the present study have been deposited under Genbank NCBI ( http://www.ncbi.nlm.nih.

Characteristics of isolates
A total of 38 microorganisms including 15 Bacillus , 12 LAB and 11 yeasts isolated from fermented food produced in different areas of Burkina Faso were studied ( Table 1 ). These fermented foods come from different sources of vegetable seeds of Adansonia digitata ( Maarri ), Parkia biglobosa ( Soumbala of Néré), Hibiscus sabdariffa ( Bikalga ), root of Manihot esculenta ( Attiéké), Glycine max ( Soumbala of Soya ) and fermented milk of animal as Camelus dromedarius (camels), Bos Taurus (cows) and Capra hircus (goats). Macroscopic observation of presumed Bacillus revealed round colonies with variable margins (regular, Table 1 Characteristics of strains used in this study.

Isolates Fermented food and locality
Cell morphology Gram Catalase Oxidase Spore Mobility AB1 Attiéké, Ouagadougou Rod-shaped, alone, in pairs and small chain Attiéké, Ouagadougou Rod-shaped, alone, in pairs and small chain Attiéké, Ouagadougou Rod-shaped, alone, in pairs and small chain Attiéké, Ouagadougou Rod-shaped, alone, in pairs and small chain Bikalga, Ouagadougou Rod-shaped, alone, in pairs and in chain Bikalga, Ouagadougou Rod-shaped, alone, in pairs and in chain Bikalga, Ouagadougou Rod-shaped, alone, in pairs and in chain Maarri, Ouagadougou Rod-shaped, in pairs and in chain Maarri, Ouagadougou Rod-shaped, in pairs and small chain Soumbala néré, Ouagadougou Rod-shaped, alone, and small chain Soumbala of néré, Ouagadougou Rod-shaped, alone, pairs and small chain Soumbala of néré, Ouagadougou Rod-shaped, alone and small chain Soumbala of néré, Ouagadougou Rod-shaped, in pairs and chain Soumbala of soya , Ouagadougou Rod-shaped, in pairs and small chain Soumbala of soya , Ouagadougou Rod-shaped, in pairs and small chain Fermented milk cow, Bobo-Dioulasso Rod-shaped, small, alone and small chain Fermented milk cow, Dori Rod-shaped, small, alone and small chain Fermented milk cow, Gorom-Gorom Rod-shaped, small, alone and small chain Fermented milk cow, Sebba Rod-shaped, small, alone and small chain Fermented milk camel, Gorom-Gorom Rod-shaped, alone, pairs and small chain Fermented milk camel, Dori Cocci, small, alone, pairs and small chain Fermented milk camel, Djibo Cocci, small, alone, pairs and small chain Fermented milk camel, Gorom-Gorom Rod-shaped, small, alone and small chain Fermented milk goat, Dori Rod-shaped, small, alone and small chain Fermented milk goat, Dori Cocci, oval, pairs and small chain Fermented milk goat, Djibo Cocci, small, alone, pairs and small chain Fermented milk goat, Sebba Rod-shaped, small, alone and small chain Fermented milk cow, Bobo-Dioulasso Ovoid, spherical, elongated, alone, pairs NT Fermented milk cow, Dori Ovoid, shape, alone, pairs small chain and heap NT Fermented milk cow, Gorom-Gorom Ovoid, spherical, alone, pairs and heap NT Fermented milk camel, Sebba Ovoid, shape, alone and heap NT Fermented milk camel, Dori Ovoid, spherical, alone and pairs NT Fermented milk camel, Gorom-Gorom Ovoid, elongated and alone NT Fermented milk camel, Djibo Ovoid, elongated, alone, pairs and heap NT Fermented milk camel, Sebba Ovoid, shape, alone and heap NT Fermented milk goat, Gorom-Gorom Ovoid, spherical, alone, pairs and heap NT Fermented milk goat, Djibo Ovoid, spherical, alone, pairs and heap NT Fermented milk goat, Sebba Ovoid, spherical, alone, pairs and heap NT + + Asc irregular) flat or curved, whitish or beige in colour with an opaque appearance. Colonies size's varies between 0.5 mm to 6 mm in diameter, spore forming, Gram-positive and, motile. Morphology colonies of presumed LAB was differed, colour varied from white to pale creamy, the shape was circular and the size varied from 0.5 to 3 mm in diameter. Only representative bacteria Gram-positive, catalase negative and not spore forming isolates were identified at species level by sequencing 16S rRNA. As for yeasts, several morphotypes i.e. white, creamy, red, smooth, rough colonies with varying edges, not motile, ovoid, spherical and sizes (1 to 7 mm) were observed. These isolates were presumptively identified as Bacillus , LAB and yeasts according to their morphology and biochemical characteristics, according to the literature.

Grouping of isolates
The strains were classified into different groups according to characteristic bands contained in their profiles genomic fingerprinting ( Table 2 ). The rep-PCR allowed the discrimination at species level for the isolates studied according to Figs. 1 -3 .
For the presumed Bacillus , five groups were observed according to Fig. 1 . Group 1 was characterized by two constant DNA bands and comprised SY3, MB9, AB5, SS1 and SS4. Group 2 was characterized by three bands with SY7 and BB11 as representing. Group 3 was characterized by two bands (BB9, SY9, AB1 and MB7). Group 4 was characterized three bands with three isolates AB7, AB6 and SY6. Group 5 (BB4) was characterized by five bands.
Based fingerprinting of Fig. 2 , the presumed LAB were classed in seven groups according to the characteristic of DNA bands ( Table 2 ). Group 1 (LCJ8, LCD3, LGJ1), group 2 (LBB6, LBG12, LBD1) and group 4 (LCG1) have two specific bands ( Table 2 ). Group 3 (LGD8) and group 5 (LGS2, LCG4) have three specific bands. Group 6 (LBS9) and group 7 (LGD9) have four bands with only one representative per group. The profile of isolate LCG1 is clearly different of other profiles obtained, having a resemblance between them.  Yeasts were classed in seven groups according to Fig. 3 . The different groups according to the characteristic of DNA bands are consigned in Table 2 . Group 1 (YGS5, YGJ2, YGG4 and YBG3) and group 5 (YCS1 and YBS15) are characterized by six specifics bands. Group 2 (YBD6), group 4 (YCJ10) and group 7 (YBB1) are characterized by one specific band and one representative per group. Group 3 (YCG7) and group 6 (YCD3) are characterized by one representative per group with two specifics bands.

Genetic identification
Similarity analysis was used to study the relationships of bacteria by comparison of 16S rRNA gene sequences with NCBI and Ezbiocloud sequences available in these databases by BLAST program.

Phylogenetic trees analysis
The phylogenetic trees have been realised to determine the taxonomic affiliation the species found in this study with reference strains. They were built by the method of distances neighbour-Joining by Blast program at 10 0 0 bootstrap. Fig. 4-6 show the relationships between Bacillus , LAB and yeasts, respectively. The phylogenetic tree based on 16S rRNA gene sequence ( Fig. 4 ) revealed that AB7 and AB6 strains were very close to B. australimaris . As for the SY7, BB7, BB9 and MB9, they are close to B. cereus . LCG1 strain is close to B. pumilus .
For the LAB ( Fig. 5 ), the phylogenetic tree based on 16S rRNA gene sequence further revealed that LCJ8 and LGD9 strains were very close to Enterococcus and Leuconostoc genus, respectively. This Fig demonstrates the phylogenetic infer relationships derived from neighbour-joining analysis of 16S rRNA gene sequences of the LBB6, LGS2 and LBS9 with highest validated described species of the genus Lactobacillus .

Discussion
Attiéké, Bikalga, Maari, Soumbala and fermented milk manufactures are based on the old empirical knowledge of several Burkinabè indigenous tribes, whose traditional methods of preparation have changed little over time. The technology of Attiéké production was exported from Ivory Coast and presumably adapted locally, resulting in many cassava-fermented products, such as Gari, fufu, lafun, dawa -dawa, chickwanghe, agbelima, kivunde and peujeum in Africa [18] . These manufactures involve many microorganisms, which are important sources for the production of bioactive substances during the fermentation. Certain bacterial and yeast are used as probiotic or biocatalysts producing compounds of interest (aromas, vitamins, antibiotics) in fermentations. Fermentation is a simple way of processing and preserving food for human consumption [19] . Among these foods, the fermented condiments and dairy products have a prominent place within the functional foods consumed in developing countries [20] . The health benefits of the microbiota of foods are due to LAB, yeasts, moulds, Bacillus , Bacteriophage and Escherichia coli Nissle 1917, which have already been demonstrated in many applications as probiotic [21] . They have long been used for their beneficial properties, including their antibacterial, anticarcinogenic, wound healing, antiallergenic, immunomodulation, and gastrointestinal immunity activities as Lactobacillus rhamnosus GG and Saccharomyces boulardii CNCM I-745. Several authors have reported that LAB and Bacillus are the majority bacteria in indigenous fermented food from Africa. These bacteria have good probiotic characteristics in terms of acid tolerance, bile tolerance, antibiotic sensitivity and antibacterial activity against pathogens [22] . The probiotic microbiome plays an important role between the gut microbial metabolism and mental health [23] .
Many studies have described LAB's and Bacillus 's ability to produce antimicrobials. These Antimicrobial peptides of LAB are the most widely used as food additives for preservation in world [24] . They are involved in both spontaneous fermentations and large-scale fermentation processes for the preservation and transformation of many raw materials from animals and vegetables.
Molecular methods are important for bacterial identification and possibly more accurate for microorganisms than the conventional phenotypic methods. Recently, new molecular tools have been applied for the routine identification of microbes, and had led to an increase in the number of identified bacteria comparatively to phenotypic and biochemical tests for identification of bacteria [25] . In these years, rep-PCR and 16S or 26S-RNA sequencing method has been proven useful for identification and characterization of bacteria and yeasts.
The rep-PCR allows good discrimination of isolates while, the 16S or 26S rRNA sequencing was performed for the molecular identification of isolates. Our findings confirmed that the rep-PCR and 16S or 26S rRNA analysis provides good discrimination of strain at species level. The alignment of these sequences for identification of microorganisms was considered at a percentage of similarity ≥ 99%. The Rep-PCR is a molecular biology tool recently used for the differentiation of microorganisms at the species level. A visual observation of results and partial sequencing rRNA allowed the differentiation of LAB in four groups ( Fig. 5 ) and yeasts in seven groups ( Fig. 6 ).
For the B. cereus group, many publications affiliate B. cereus actually as B. cereus s.l. because these species are very indistinguishable by 16S rDNA sequencing. This group has the diverse faces according to activity for food-borne intoxications and playing the role of probiotic. B. cereus s.l. consists of eight species: B. anthracis, B. pseudomycoides, B. mycoides, B. thuringiensis,  B. weihenstephanensis, B. cytotoxicus, B. toyonensis, B. megaterium and B. cereus s. stricto . Several authors reported B. cereuslike enterotoxins from non-Bacillus cereus species of the genus, but without providing a conclusive identification of those toxins. Presently, their classification rely mainly on distinctive phenotypic traits, such as pathogenic potential to mammals, enzymatic ability causing food spoilage, thermotypes, as well as colony morphology. Despite their pathogenicity, B. cereus might be an excellent candidate for bioremediation, detoxification of Aflatoxin from both field and food matrices, production of L -lactic acid and antibacterial peptides [26 , 27] . In this study, the presumed LAB were genotypically grouped by GTG 5 based rep-PCR fingerprinting. Only isolate presumed LAB was revealed to Bacillus after sequencing 16S rRNA. Satomi et al. [28] reported that B. pumilus group have a similarity rate of 99.9% for 16S rRNA gene sequencing in the Planetary Protection archive. In this study, AB7 and LCG1 were high the percentage of similarity to B. safensis (99.37%) and B. australimaris (99.14%), respectively. Bacillus species are the species microbial difficult to differentiate by conventional methodologies and represent the most widespread terrestrial species microbial [29 , 30] . According to Branquinho et al. [29] , the using of MALDI-TOF MS analysis was able to resolve taxonomic identifications of bacteria that are indistinguishable by 16S rRNA sequences. But, the combined of MALDI-TOF-MS and chemometric approach has clearly discriminated B. pumilus and B. safensis [29 , 31] A combination of the results obtained with rep-PCR and sequencing showed that eleven species of LAB of this study was affiliated to genus Lactobacillus ( Fig. 5 ) . Alegría et al. [32] reported that the rep-PCR allowed a differentiation between sub species of Lactococcus lactis . The Lactobacillus plantarum group was identified as the predominant flora in samples studied. According to Fig. 5 , the genus Lactobacillus (66.67%) are the highest, followed by genus Enterococcus (16.67%) and Leuconostoc (16.66%). Moreover, other genera, namely, Pediococcus, Weisella , and Lactococcus , were not detected in these isolates. The development of biopreservation technologies using LAB and their metabolites represents an additional hurdle in the protection of food against microbial contamination as these bacteria produce several antimicrobial substances including organic acids, hydrogen peroxide and bacteriocins [33] . However, the use of LAB for this purpose requires confirmation of the safety of strains, as well as their virulent potential, in order to ensure the safety of consumers [34] . LAB are commonly part of the microbiota of fermented foods and beverages due to their important role in the technological aspects of foods maturation and contribution to the sensorial characteristics of these foods. LAB are known to be able to produce many bioactive compounds used in several fields of life. They are considered as biopreservative tool to control the growth of spoilage-related and pathogenic bacteria [22 , 35] .
According to their profile ( Fig. 3 ), yeasts belonged to the genera most frequently highlighted in dairy products: Candida, Kluyveromyces, Pichia, and Rhodotorula. Pichia kudriavzevii was once called Issatchenkia orientalis [36] . Cyberlindnera fabianii is used in wastewater treatment and fermentation of alcoholic beverages. Miao et al. [37] have reported the presence of Issatchenkia orientalis in tropical fruit and food sources and traditional African fermented foods. Koutinas et al. [38] have reported than Issatchenkia orientalis produce ethanol and have higher thermotolerance, salt tolerance, and acid tolerance than Saccharomyces cerevisiae . This later has an ability on the reduction of Aflatoxin M1 in milk [39] . Fermentation, by certain LAB, Bacillus and yeasts, removes or reduces the levels of antinutritional factors such as phytic acid, tannins and polyphenols present in foods and releases minerals such as manganese, iron, zinc and calcium. This fermentation reduces also the cyanogenic toxicity and enhances flavour, taste and aroma of the fermented products. This strategy allows native microbes to degrade contaminants and co-substrates [40] .
Although identification of microorganisms is currently based on 16S rRNA sequencing, it remains low for discrimination in some genera. The microbiota of fermented food analysed have a very heterogeneous and exploitable microbial diversity in the field to research the new probiotic starters. This microbial diversity and the presence of opportunistic pathogens in the fermented food and milk are due to various sources of contamination (mammary glands, udder skin, raw material, milking means, air quality of farm and the practices of producers).

Conclusion
Traditional fermented foods products have high prebiotics and probiotic activity. The fermented food product based on seed, roots and fermented milk of animals from Burkina Faso was confirmed to be rich in Bacillus , LAB and yeast. B. pumilus, B. cereus, Enterococcus durans, Lactobacillus paracasei, Lactobacillus plantarum, Leuconostoc pseudomesenteroides, Saccharomyces cerevisiae and Kluyveromyces marxianus are the most studied strains and used as probiotics . These microorganisms are involved in both spontaneous fermentations and large-scale fermentation processes for the preservation and transformation of many raw food materials. Their metabolites may contribute to characteristics these fermented foods. Thus, the fermented milk and seeds are important sources of foods contributing to resolve the problems of diseases in world developing countries.

Declaration of Competing Interest
The authors declare that there is no conflict of interest and confirm that this manuscript does not infringe any other copyright or property rights. All authors agreed to publication of the work.