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International Journal of Chemical Studies 2019; 7(3): 3282-3288

P-ISSN: 2349–8528
E-ISSN: 2321–4902
IJCS 2019; 7(3): 3282-3288 Isolation, characterization and screening of novel
© 2019 IJCS
Received: 15-03-2019 antibiotic producing bacteria from natural
Accepted: 20-04-2019
habitats of Western Himalayas and industrial
Yog Raj
1. Department of Microbiology
waste soil samples
Himachal Institute of Life
Sciences, Paonta Sahib,
Himachal Pradesh, India Yog Raj, V Singh and Arti Chauhan
2. Agrotechnology of Medicinal,
Aromatic and Commercially
Abstract
Important Plants Division,
Antibiotics, potential against multi-drug resistant (MDR) pathogenic bacteria is currently become a vital
CSIR-IHBT, Palampur,
Himachal Pradesh, India research area. The present research approach is focused on the isolation of antibiotic producing bacteria
from the soil samples collected from several diverse habitats viz. preserved areas of Himalayas, natural
V Singh water resources, rhizosphere of medicinal plants, agricultural soil, forest soils, industrial waste soil from
Department of Microbiology district Kullu and Poanta Sahib (HP). The bacterial isolates were characterized on the basis of their
Himachal Institute of Life morphology, further confirmed by biochemical and haemolytic activity tests. Antibiotic producing ability
Sciences, Paonta Sahib, of isolates was confirmed by zone of inhibition around bacterial colonies. A total of 30 isolates belonging
Himachal Pradesh, India to six different genera i.e. Micrococcus, Bacillus, Lactococcus, Pseudomonas, E.coli and Proteus,
antibiotic producing bacteria were found in different soil samples. Out of these, 12 potential antibiotic
Arti Chauhan producing strains showed their inhibitory response against pathogenic microorganisms. These results
Department of Microbiology suggested that after proper standardization and processing, soil isolates having antibiotic producing
Himachal Institute of Life capability can be used commercially.
Sciences, Paonta Sahib,
Himachal Pradesh, India
Keywords: Antibiotics, MDR, haemolytic activity, rhizosphere, zone of inhibition

Introduction
The word “antibiotic” is derived from Greek term antibiosis which means “against life”.
Antibiotics are medicine that kill or prevent the growth of bacteria, used to cure diseases. More
than 4000 antibiotics have been isolated, but only 50 have achieved wide usage while rest of
the other antibiotic compounds being toxic to humans and animals, high production costs
failed to attain commercial importance [1]. Antibiotics are natural drugs produced by several
fungi or bacteria unlike chemotherapeutic drugs which are manmade substances. Antibiotics
have long been considered the “magic bullet” that would end infectious disease.
Antimicrobial drugs are generally classified into two categories; one includes the synthetic
drugs, such as sulfonamides and quinolones, the second antibiotics synthesized by
microorganisms. Antibiotics, potential against multi-drug resistant (MDR) pathogenic bacteria
is currently become a vital research area. Natural bioresources having novel structures have
been observed to retain valuable biological activities. Producers of antibiotic can be found in
rivers, lakes, decaying plants and animal remains etc. but majority of microorganisms that
produce antibiotic inhabits soil. Many species of Bacillus are of considerable importance due
to antibiotic producing abilities [2]. Bacillus sp. produces diverse range of antibiotics such as
bacitracin and gramicidin which is produce by Bacillus licheniformis and Bacillus brevis
respectively. These antibiotics are active against many gram positive organisms such as
Stapylococci, Streptococci, anaerobic cocci, Cornyebacter and Clostridia but not against most
Correspondence
Yog Raj other gram negative bacteria [3]. Nowadays, much attention has been given to the increase in
1. Department of Microbiology antibiotic resistance as several microbial species and strains become resistant, many diseases
Himachal Institute of Life have become difficult to treat. Research in finding newer antibiotics and enhancing
Sciences, Paonta Sahib, productivity of such agents has become an essential action [4, 5]. The vast majority of novel
Himachal Pradesh, India
antibiotics have been detected by screening of “wild isolates” acquired from soil and other
2. Agrotechnology of Medicinal,
Aromatic and Commercially natural habitats.
Important Plants Division, The present study directed the isolation and screening of potential antibiotic producing bacteria
CSIR-IHBT, Palampur, from soil, optimization and characterisation of antibiotic producing strain, production of
Himachal Pradesh, India antibiotics by recovered strain, determining the prevalence of recovered isolates and to check
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antimicrobial activity of recovered isolates against some light microscope under 100x oil emersion objective to observe
pathogenic bacteria viz. Pseudomonas (2488), Proteus (425), the colour, shape, size and arrangement of bacterial cells.
Streptococcus (655), Bacillus cereus (1305) and
Staphylococcus (96). Biochemical Characterization
The various biochemical tests viz., Indole, Methyle Red,
Material and Methods Voges Proskaur, Citrate utilization testes were carried out for
The present study was carried out in the Department of identification of isolates. Cappuccino Sherman’s Manual of
Microbiology, Himachal Institute of Life Sciences, Poanta Microbiology, 7th Ed [6].
Sahib (HP).
IMVIC Test
Collection of Soil Sample Indole Test
In systematic screening for isolation of antibiotic producing Bacterial colony was inoculated in 1% tryptophan broth in a
bacteria a total 22 soil samples were collected from several test tube. After incubation period of 48 h at 37 0C, one
diverse habitats viz.preserved areas of Himalayas, Natural millilitre (1ml) of chloroform was added to the broth. The test
water resources, rhizosphere of medicinal plants, agricultural tube was shaken gently, then 2.1 ml of Kovac’s reagent were
soil, forest soils,industrial waste soil from district Kullu and added and this was also shaken gently and allowed to stand
Poanta Sahib (HP). The samples were taken after removing for 20 min. The formation of red colouration at the top layer
approximately 3 cm of the soil surface, deep up to 20 cm as indicated positive and yellow colouration indicates negative.
most of the bacterial population is concentrated on upper
layer of the soil. Soil samples were collected with sterile Methyl Red
spatula in clean dry and sterile polythene bags, transferred to The isolates were inoculated in MR-VP medium and
the Department of Microbiology, HILS at Poanta Sahib and incubated at 37 0C for 24 h. Few drops of methyl red reagent
kept at 4 0C for further processing. were added after incubation of 24 h. The presence of red
colour indicated positive test.
Processing of Samples
Soil samples (50g each) were dissolved in 100 ml of sterile Voges Proskauer Test
distilled water to make soil suspensions and after that with the The isolates were inoculated in MR-VP medium and
help of Whatman filter paper obtained almost clear solution incubated at 370C for 24 h. After 24 h, 3 drops of 40% KOH
devoid of soil, stones and debris. Then filtrated solution was and 9 drops of alpha-naphthol reagent were added.
serially diluted to ten folds. Appearance of red colour showed positive test.

Isolation and Sub Culturing of Bacteria Citrate Utilization Test


The nutrient agar medium was used for the isolation of Isolates were streaked on Simmon citrate slants and incubated
bacteria; 28g of nutrient agar powder dissolved in 1000 ml of at 37 0C for 24 h, appearance of blue colour indicated for
distilled water, sterilized in autoclave for 15 min. at 121 0C positive test.
after cooling poured in Petri dishes and allowed to solidify.
Portions of the soil suspension (100 μl) inoculated on the Haemolytic Activity/ Blood Agar Culture
nutrient agar media by spread plate method were incubated at For the identification of pathogenic and non-pathogenic
370C for 24h. Bacterial colonies with clear zone were isolates, growth of bacteria was studied on blood agar by
observed and further sub cultured into nutrient agar slants preparing sterile plates of blood agar media, adding 10% of
using a sterile wire loop, incubated at 37 0C for 24h for blood in media. Subsequently streak isolated strains on the
preservation and purify the isolates. These slant bottles plates. Incubate the plates for overnight at 370C and study the
containing the bacterial isolates were kept in refrigerator at 4 growth of bacteria on plates.
0
C for short time storage prior biochemical tests for
identification. Screening for Anti-Microbial Activity
In present investigation of antibiotic production was studied
Identification of Bacterial Strains under different time periods i.e., 1 to 20 days of incubation.
The selected strains were identified by means of physical, Screening are based on the using the broth cultures of
biochemical and haemolytic characterisation. antibiotic producing strains in agar well diffusion method and
their supernatants separately in case of disc diffusion method.
Physical Characterization
Colony Morphology Agar Well Diffusion Method
Shape, size, colour, elevation, margin of colony and Prepare 5 test tubes, each containing 5 ml of MHB (Muller
appearance were observed in overnight plate culture and Hinton Broth). After autoclaving, pathogenic strains were
noted down. inoculated and kept in incubator at 370C for 24 h.
Subsequently the recovered isolates were inoculated in NB
Gram Staining (Nutrient Broth) after autoclaving. It was kept on shaker for
Thin smear of bacterial culture was prepared and then heat 48 h. Spread100l of pathogenic strain on MHA (Muller
fixed. Few drops of Crystal Violet were added on the smear Hinton Agar) plates with the help of sterile glass spreader.
for 60 sec. and removed with distilled water. The smear was Then bore wells of 6 mm diameter on the MHA plates, pour
then covered with Gram’s iodine solution for 60 sec. and then the isolates in to the wells with the help of micropipette. The
the smear was treated with alcohol followed by counterstained plates were kept for 48 h incubation period after that
with safranin dye to the smears for 30 sec. Slide was then inhibition zones were observed.
washed with distilled water and let it air dry, observed under

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Disc Diffusion Method inhibition against five bacterial pathogens after 48 h of


Recovered isolates were inoculated in 50 ml nutrient broth incubation period. Out of 30 strains 5 potential antibiotic
and was kept in a rotatory shaker at 37 0C for 48 h. After 48 h producing strains (APS-3, 9, 12, 15, 17) showed zone of
decant the 5 ml of broth culture into eppendorf test tubes and inhibition 14, 20, 16, 29 and 10 mm respectively against
centrifuged at 5000 rpm for 10 min. at 4 0C.The 5 pathogenic pathogenic strain Pseudomonas (2488). In case of
strains were grown in MHA having 100μl of inoculum. Small Streptoococcus (655),7 strains (APS-1, 3, 4, 6, 7, 12, 17)
discs were punched out from filter paper and were spreaded showed clear zone of inhibition of 16, 21, 17, 12, 17, 14, 10
on the MHA plates. The filter discs were dipped in the mm for Bacillus and Staphylococcus 6 strains (APS-1, 3, 4, 7,
centrifuged broth culture in eppendorf tube for 10 to 15 15, 17) and only 3 strains (APS-3, 4, 6) showed clear zone of
minutes prior to the placement of discs on MHA plates. The inhibition of 18, 12, 12, 10, 11, 15 mm and 20, 10, 22 mm
plates were kept for incubation of 48 h. Zone of inhibitions respectively while there were no zone of inhibition observed
were observed around the filter paper. against Proteus (425) (Fig. 4a-f and Table 4). In previous
report [11] discovered the production of bacitracin and subtillin
Result and Discussion by Bacillus sp. Similarly [12] investigated that bacitracin
Isolated Microorganism from Soil Sample produced by Bacillus sp. inhibits Escherichia coli and
In the course of screening of novel antibiotic producing Staphylococcus aureus. Whereas [8] reported isolates Bacillus
bacteria from soil samples, many antibiotic producing cultures alvei, Enterobacter aerogene, Micrococcus roseus showed
were recovered from soil sample taken from Poanta sahib and inhibitory response towards S. aureus, Pseudomonas sp. and
district Kullu (HP). In the present study, total 30 Shigella sp. with clear zone of inhibition 15, 17 and 12 mm
phenotypically different strainspossessing capability to respectively.
producing antibiotics were isolated on NA medium (Nutrient
Agar)from 22 soil samples, showingcolonies with clear zone Disc Diffusion Method
after incubationperiod of 24 hat 37 0C. Colonies which showed In this experiment, small disc were punched out from a sterile
clear zone were preserved on NA slants for further use. In a filter paper and dipped in the centrifuged broth culture of
study [7] a total 56 isolates having potential to produce recovered isolates in 5ml eppendorf test tube for 10 to 15 min.
antibiotic were recovered from 25 soil samples collected from then placed on MHA plates for observation of clear zone after
different areas of Lahore. In earlier study [8] reported 10 48 h of incubation. Result revealed that APS-12, 17 showed
bacterial isolated from different location within Birnin Kebbi inhibitory activity againstpathogenic strain Pseudomonas
metropolis from which only 5 (50%) of isolates were active. (2488) having zone 10 and12 mm. APS-1, 3, 12 showed
inhibition zone of 14, 15, 10 mm against Streptococcus (655).
Characterization of Selected Isolates For Bacillus and Staphylococcus APS-5 and APS-3, 6 showed
Recovered 30 isolates were characterized and identified by zone of 14 mm and 10, 17 mm respectively (Fig. 5 and Table
their physical characterization, possessing white, yellow and 5). In other study [13] investigated, two isolates 5 and 6
mucoid colony having rod and cocci shape (Table1), inhibited the growth of S. aureus and P. vulgris with zone
morphological examinations of isolates are much similar to having diameter of 11 and 12 mm respectively.
earlier study [9]. Gram staining of recovered isolates showed
12 strains gram negative for reaction showing pink colour and Conclusion
rest 18were found gram positiveshowing blue or purple colour The soil microbial isolate were showing antibiotic activity
under light microscopy (Fig.1 and Table 2). Biochemical under normal growth conditions was found inhibiting
characterisation coupled with Bergery’s Manual of pathogenic strains of the gram positive bacilli and cocci. The
Determinative Bacteriology [10] conferred the presence of present data focused on obtaining local microbial isolates
bacteria probably to the genera Micrococcus, Bacillus, which have the ability to produce antimicrobial agent.
Lactococcus, Pseudomonas, E.coli and Proteus (Fig. 2a-c and Exposing potential antibiotic producing strains with
Table 3). competing organisms, its production can be enhanced. Based
Haemolytic test showed that out of 30 isolates, 12 were non- on the above experimental study, we reached to the following
pathogenic i.e. they showed  haemolysis, while the other 18 conclusions that the strain APS-15 was found to be having
were pathogenic i.e. they showed  and  haemolysis (Fig.3). better antimicrobial activity against Pseudomonas in
comparison with other soil isolates, which have been
Screening for Antibacterial Activity investigated. APS-12 and APS-17 showed minimum zone of
Results are based on the screening of antimicrobial activity inhibition against Staphylococcus. Proteus showed resistance
using the cultures of antibiotic producing strains in agar well to all isolates. It is concluded that Bacillus species and
diffusion method and their supernatants separately in case of Micrococcus sp. isolated during the course of this research
disc diffusion method. It was found that maximum zone of from soil samples have potential of produce antibiotics. These
inhibition showed by recovered isolatesafter an incubation results suggested that after proper standardization and
period of 7 days. processing, soil isolates having antibiotic producing capability
can be used commercially.
Agar Well Diffusion Method
Antibiotics produced by the isolates showed variable zones of

Table 1: Morphological Characterization of Recovered Isolates


Sr. No. Characters Morphology
1 Colour White, Yellow, creamish and mucoid with clear zone
2 Colony size Medium
3 Shape Rod and cocci shape

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Table 2: Gram Staining Characterization of Recovered Isolates Table 4: Antimicrobial Activity of Isolates by Agar Well Diffusion
Method
Strain Colour and Morphology Type and Bacteria
APS-1 Pink and Micrococci Gram Negative Zone of inhibition in mm
APS-2 Blue and Micrococci Gram Positive Bacillus
Isolates Pseudomonas Proteus Streptococcus Staphylococcus
cereus
APS-3 Pink and Bacilli Gram Negative (2488) (425) (655) (96)
(1305)
APS-4 Blue and Micrococci Gram Positive APS-1 N.Z N.Z 16 18 N.Z
APS-5 Pink and Bacilli Gram Negative APS-2 N.Z N.Z 6 N.Z N.Z
APS-6 Pink and Bacilli Gram Negative APS-3 14 N.Z 21 12 20
APS-7 Blue and staphylococci Gram Positive APS-4 N.Z N.Z 17 12 10
APS-8 Blue and staphylococci Gram Positive APS-5 N.Z N.Z N.Z 8 8
APS-9 Blue and Micrococci Gram Positive APS-6 N.Z N.Z 12 9 22
APS-10 Blue and staphylococci Gram Positive APS-7 N.Z N.Z 17 10 N.Z
APS-8 N.Z N.Z 9 N.Z N.Z
APS-11 Blue and staphylococci Gram Positive
APS-9 20 N.Z N.Z 5 N.Z
APS-12 Blue and staphylococci Gram Positive APS-10 N.Z N.Z N.Z N.Z N.Z
APS-13 Pink and staphylococci Gram Negative APS-11 N.Z N.Z N.Z N.Z N.Z
APS-14 Blue and Bacilli Gram Positive APS-12 16 N.Z 14 N.Z 3
APS-15 Blue and staphylococci Gram Positive APS-13 N.Z N.Z N.Z N.Z N.Z
APS-16 Blue and Bacilli Gram Positive APS-14 N.Z N.Z N.Z N.Z N.Z
APS-17 Blue and staphylococci Gram Positive APS-15 29 N.Z 9 11 N.Z
APS-18 Blue and Micrococci Gram Positive APS-16 N.Z N.Z N.Z N.Z N.Z
APS-19 Blue and Micrococci Gram Positive APS-17 10 N.Z 10 15 3
APS-18 N.Z N.Z N.Z N.Z N.Z
APS-20 Pink and staphylococci Gram Negative
APS-19 N.Z N.Z N.Z N.Z N.Z
APS-21 Blue and Bacilli Gram Positive APS-20 N.Z N.Z N.Z N.Z N.Z
APS-22 Blue and Bacilli Gram Positive APS-21 N.Z N.Z N.Z N.Z N.Z
APS-23 Pink and Micrococci Gram Negative APS-22 N.Z N.Z N.Z N.Z N.Z
APS-24 Pink and staphylobacilli Gram Negative APS-23 N.Z N.Z N.Z N.Z N.Z
APS-25 Blue and staphylobacilli Gram Positive APS-24 N.Z N.Z N.Z N.Z N.Z
APS-26 Pink and Micrococci Gram Negative APS-25 N.Z N.Z N.Z N.Z N.Z
APS-27 Pink and staphylobacilli Gram Negative APS-26 N.Z N.Z N.Z N.Z N.Z
APS-27 N.Z N.Z N.Z N.Z N.Z
APS-28 Blue and Micrococci Gram Positive
APS-28 N.Z N.Z N.Z N.Z N.Z
APS-29 Pink and staphylobacilli Gram Negative APS-29 N.Z N.Z N.Z N.Z N.Z
APS-30 Pink and Bacilli Gram Negative APS-30 N.Z N.Z N.Z N.Z N.Z
N.Z-No Zone
Table 3: Biochemical Characterization of Isolates
Table 5: Antimicrobial Activity of Isolates by Disc Diffusion
Isolates Indole MR VP Citrate Utilization Probable identified Species
Method
APS-1 - + - + Micrococcus roseus
APS-2 - - - - Bacillus/ Micrococcus luteus Zone of inhibition in mm
APS-3 - + - - Lactococcus lactis Pseudomonas Proteus Streptococcus Bacillus cereus Staphylococcus
Isolates
APS-4 - - - - Bacillus/ Micrococcus luteus (2488) (425) (655) (1305) (96)
APS-1 N.Z N.Z 14 8 N.Z
APS-5 - + - - Lactococcus lactis
APS-2 N.Z N.Z 6 N.Z N.Z
APS-6 - + - + Micrococcus roseus APS-3 N.Z N.Z 15 N.Z 10
APS-7 - - - - Bacillus/ Micrococcus luteus APS-4 N.Z N.Z N.Z N.Z N.Z
APS-8 - + - - Bacillus/ Micrococcus luteus APS-5 N.Z N.Z N.Z 14 N.Z
APS-9 - - - - Bacillus/ Micrococcus luteus APS-6 N.Z N.Z N.Z N.Z 17
APS-10 - + - - Lactococcus lactis APS-7 N.Z N.Z 6 9 N.Z
APS-11 - - - - Bacillus/ Micrococcus luteus APS-8 N.Z N.Z 6 N.Z N.Z
APS-12 - + - + Micrococcus roseus APS-9 N.Z N.Z N.Z N.Z N.Z
APS-13 - - - + Pseudomonas aeruginosa APS-10 N.Z N.Z N.Z N.Z N.Z
APS-11 N.Z N.Z N.Z N.Z N.Z
APS-14 - - - + Pseudomonas aeruginosa
APS-12 10 N.Z 10 8 N.Z
APS-15 - - - - Bacillus/ Micrococcus luteus APS-13 N.Z N.Z N.Z N.Z N.Z
APS-16 + + - - E.coli/Proteus vulgaris APS-14 N.Z N.Z N.Z N.Z N.Z
APS-17 - + - - Lactococcus lactis APS-15 5 N.Z 8 N.Z N.Z
APS-18 - - - + Pseudomonas aeruginosa APS-16 N.Z N.Z N.Z N.Z N.Z
APS-19 - + - - Lactococcus lactis APS-17 12 N.Z N.Z N.Z N.Z
APS-20 - - - - Bacillus/ Micrococcus luteus APS-18 N.Z N.Z N.Z N.Z N.Z
APS-21 - - - - Bacillus/ Micrococcus luteus APS-19 N.Z N.Z N.Z N.Z N.Z
APS-20 N.Z N.Z N.Z N.Z N.Z
APS-22 - - - - Bacillus/ Micrococcus luteus
APS-21 N.Z N.Z N.Z N.Z N.Z
APS-23 - - - - Bacillus/ Micrococcus luteus APS-22 N.Z N.Z N.Z N.Z N.Z
APS-24 - + - + Micrococcus roseus APS-23 N.Z N.Z N.Z N.Z N.Z
APS-25 - + - - Lactococcus lactis APS-24 N.Z N.Z N.Z N.Z N.Z
APS-26 - + - - Lactococcus lactis APS-25 N.Z N.Z N.Z N.Z N.Z
APS-27 - - - - Bacillus/ Micrococcus luteus APS-26 N.Z N.Z N.Z N.Z N.Z
APS-28 - - - - Bacillus/ Micrococcus luteus APS-27 N.Z N.Z N.Z N.Z N.Z
APS-29 - - - - Bacillus/ Micrococcus luteus APS-28 N.Z N.Z N.Z N.Z N.Z
APS-30 - - - + Pseudomonas aeruginosa APS-29 N.Z N.Z N.Z N.Z N.Z
APS-30 N.Z N.Z N.Z N.Z N.Z
APS-Antibiotic producing strain

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Fig 1: Gram staining of recovered isolates

A. Control B. Positive result C. Negative result


Fig 2: Biochemical characterization of isolates

Fig 3: Haemolytic activities of recovered isolates

Fig 4b: Antibiotic producing strains (APS-1, 3, 4, 6, and 7) showing


zone of inhibition against pathogenic strain Streptococcus (655)

Fig 4a: Antibiotic producing strains (APS-3, 9, 12, 15, and 17) Fig 4c: Antibiotic producing strains (APS-1, 3, 4, 15, and 17)
showing zone of inhibition against pathogenic strain Pseudomonas showing zone of inhibition against pathogenic strain Bacillus cereus
(2488) (1305)

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Fig 4d: Antibiotic producing strains (APS-3, 4,5, 6 and 12) showing
zone of inhibition against pathogenic strain Staphylococcus (96) Fig 4e: Control plate

Fig 4: Isolates showing antimicrobial activity againstpathogenic test organism in agar well diffusion method

Fig 5a: Antibiotic producing strain (APS-5) showing zone of


Fig 5c: Antibiotic producing strains (APS-3, 6) showing zone of
inhibition against pathogenic strain Bacillus cereus (1305)
inhibition against pathogenic strain Staphylococcus (96)

Fig 5b: Antibiotic producing strains (APS-1, 3, 12) showing zone of Fig 5d: Antibiotic producing strains (APS- 12, 17) showing zone of
inhibition against pathogenic strain Streptococcus (655) inhibition against pathogenic strain Pseudomonas (2488)

Fig 5: Isolates showing antimicrobial activity against pathogenic test organism in disc diffusion method

Acknowledgement and support throughout my project work. I am obliged for his


With abundant pleasure and deep sense of appreciation, I persistent, selfless devotion towards the progress of my
express my heartiest thanks to my guide Dr Virender Singh, project work and his immense endurance to listing my
Head, Department of Microbiology, Himachal Institute of problems and provide an appropriate solution for them.
Life Sciences Paonta Sahib (HP) for his exceptional guidance

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