An In silico Analysis of Deleterious Single Nucleotide Polymorphisms of Human Lysozyme C Gene |Chapter 1 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 Background: Single nucleotide polymorphisms (SNPs) play a critical role in

influencing a person's susceptibility to diseases and in determining how an

individual reacts to various treatment options. It is crucial to differentiate and

characterize damaging SNPs from neutral ones and the aim of this study was to

predict the deleterious SNPs of the lysozyme C (LYZ C) gene via an in silico

analysis. LYZ C is an important antimicrobial peptide capable of damaging the

peptidoglycan layer of bacteria leading to osmotic shock and cell death.

Methods: The missense nonsynonymous SNPs (nsSNPs) of the LYZ C gene were

subjected to different computational tools- SIFT, PolyPhen v2, SNAP, PROVEAN, 

PhD-SNP, and SNPs & GO. Deleterious SNPs as predicted by these tools were

examined by I-Mutant 3.0 and ConSurf. GeneMANIA and STRING tools were used

to study the interaction network of the LYZ C gene. The impact of variations on the

structural characteristics of the protein was studied by HOPE analysis. The

structures of variants and wild types were predicted by the SWISS-MODEL web

server and the TM-align tool was used to predict the root mean square deviation

(RMSD) and template modeling (TM) scores.

Results: Eight missense nsSNPs (T88N, I74T, F75I, D67H, W82R, D85H, R80C,

and R116S) of the LYZ C gene were found to be potentially deleterious. I-mutant

3.0 determined the variants that decreased the stability of the protein. ConSurf

predicted rs121913547, rs121913549, and rs387906536 nsSNPs to be conserved.

Interaction network tools showed that LYZ C protein interacted with lactoferrin

(LTF). HOPE tool analyzed differences in physicochemical properties between

wild type and variants. TM-align tool predicted the alignment score and the protein

 

folding was found to be identical. PYMOL was used to visualize the

superimposition of variants over wild types. 

Conclusion: The present study ascertained the deleterious missense nsSNPs of

the LYZ C gene and could be used in further experimental analysis. These high

risk nsSNPs could be used as molecular targets for diagnostic and therapeutic

interventions.

 

Author(s) Details

 

Harini Venkata Subbiah

Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher

Education and Research, Chennai, Tamil Nadu, 600100, India.

 

Dr. Usha Subbiah

Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher

Education and Research, Chennai, Tamil Nadu, 600100, India.

 

Please see the link here:- https://doi.org/10.9734/bpi/rpmab/v3/3602G

Antimicrobial Properties of Homo Fermenting Lactic Acid Bacteria (LAB) Isolated from Kunu-Zaki (A Spontaneously Fermenting Nigerian Cereal Beverage) | Chapter 8 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 Aim: The present study aimed to determine the antibiotic reaction and adhesion

pattern of antimicrobial homo-fermenting LAB strains in the fermenting slurries of

kunu-zaki, Nigeria.

Background: Lactic acid bacteria are usually found in decomposing plants and

lactic products. Lactic acid is the major metabolic end-product of the carbohydrate

fermentation. LAB is a large group of fermentative, anaerobe aero-tolerant

microorganisms that are usually present in the gut of humans and other animals,

raw vegetables, meat and meat products, and cereal.

Study Design: Samples were obtained directly from the 72-hour fermenting mash

of the kun-uzaki made from each cereal type. The Pour plate technique was used

to isolate the organisms. The pure colonies isolates were examined according to

their colony morphology, catalase reaction and gram reaction. Inhibition of

indicator lawn used ≥10mm inhibition as antibiotic susceptible. Adhesion was

measured by staining and quantifying grains of Digitariaexilis (acha), Sorghum

bicolour (sorghum) and Pennisetum americanum (millet) in composite and non

composite proportions. LAB isolates were obtained on MRS agar. Homo

fermenting isolates were identified at species level using the API 50 CHL test kit.

Antibiotic sensitivity testing on the identified isolates followed the modified

standard Kirby-Bauer procedure on MRS agar (pH 7.4) using the disc diffusion

technique with selected antibiotics. For quality control of the antibiotics, sensitive

reference strains S. aureus ATCC 25923 and E. coli ATCC 25922 obtained from

the Nigeria Institute of Medical Research were used. Adhesion properties were

determined by differential staining of the bacterial cells that bound to intestinal

epithelial cells as observed under light and phase contrast microscopy. 

Results: Antimicrobial substances produced by the eight LAB isolates inhibited

the growth of four selected human pathogens in vitro. All eight LAB isolates were

resistant to amoxicillin, gentamycin and ciprofloxacin. L. plantarum126, L.

paracasei sub sp paracasei339 and Pediococcus damnosus32 were resistant to

erythromycin whilst all others were susceptible. L. plantarum126 and L.

paracaseisubspparacasei339 were resistant to all antibiotics tested. All LAB

isolates demonstrated high in-vitro intestinal epithelial cell adhesion potential. The

result of this study documents findings on the antibiotic resistance pattern of these

eight homo-fermenting lactic acid bacteria present in ready to drink kunu-zaki. If

these homo-fermenting strains are to be used in kunu-zaki as starter cultures, it is

important that they should be further carefully examined for inability to transfer

antibiotic resistance genes to food pathogens.

Conclusion: When used in conjunction with these antibiotic treatments, kunuzaki

may not have an impact on the antibacterial activity of LAB. To ensure that these

LAB strains cannot pass antibiotic resistance genes to food pathogens, they must

be thoroughly screened if they are to be used as kunu-zaki starter cultures.

 

Author (s) Details

S. O. Oluwajoba

Department of Microbiology, Federal University of Technology, Akure, Nigeria and Department of Biological Science, Yaba College of Technology, Yaba, Lagos, Nigeria.

F. A. Akinyosoye

Department of Microbiology, Federal University of Technology, Akure, Nigeria.

V. O. Oyetayo

Department of Microbiology, Federal University of Technology, Akure, Nigeria.

Please see the link - https://doi.org/10.9734/bpi/rpmab/v3/211

Meat Starter Culture | Chapter 5 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 Meat starter cultures are maturation and surface starters used to accelerate the

fermentation process, maximize the quality, and guarantee uniformity and safety

of the product. This review discusses the beneficial role of meat starter cultures

in the acceleration and promotion of the fermentation process by rapid matrix

acidification, standardization of the product properties, improvement in

organoleptic properties, enhancing microbiological and chemical safety by

inhibiting the growth of pathogenic organisms and limiting the formation of

biogenic amines, nitrosamines, and polycyclic aromatic hydrocarbons.  The

recent advances in genomics and molecular biology of industrially useful

microorganisms with the desirable functional and protective features and rational

improvement of the starter strains to develop product-specific starter cultures

have been highlighted.

 

Author (s) Details

Dr. Rajendra Nath Borpuzari (Professor)

Department of Livestock Products Technology, Assam Agricultural University, College of Veterinary

Science, Khanapara, Guwahati - 781022, India.

 

Dr. Trishna Borpuzari (Professor (Retd.)

Department of Livestock Products Technology, Assam Agricultural University, College of Veterinary

Science, Khanapara, Guwahati - 781022, India.

 

Dr. Rashmi Rekha Saikia (Assistant Professor)

Department of Livestock Products Technology, Assam Agricultural University, Lakhimpur College of

Veterinary Science, Joyhing, North-Lakhimpur- 787051, India.

 

Please see the link :-  https://doi.org/10.9734/bpi/rpmab/v3/8092E

Microbial Challenges in Fresh-cut Produce: A Comprehensive One Health Approach | Chapter 7 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 

Food safety is a paramount concern for public health globally, particularly with the

burgeoning food markets and complex manufacturing chains. With the increasing

popularity of ready-to-eat foods, such as freshly chopped fruits and salads, the risk

of foodborne illnesses escalates, necessitating a comprehensive approach from

farm to fork. This chapter underscores the importance of adopting a One Health

strategy to prevent and control the spread of foodborne pathogens, especially in

minimally processed fruits and vegetables consumed raw. Despite their health

benefits, these foods pose significant microbiological risks due to inadequate

disinfection and oversight of transmission routes. The chapter synthesizes existing

knowledge on microbiological contamination, notable outbreaks, bacterial strains,

and mitigation strategies, spanning from production to consumption. It also

addresses challenges associated with food modification, disinfection, and

contamination sources at various stages, offering insights valuable to researchers

and food producers invested in enhancing food safety and quality.

 

Author (s) Details

Maria Isabel Santos

Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal.Faculty of Veterinary Medicine, CECAV—Centre of Animal and Veterinary Science, Lusófona University, 1749-024 Lisbon, Portugal.

 

Madalena Grácio

Instituto Superior de Agronomia, University of Lisbon, 1349-017 Lisbon, Portugal.

 

Mariana Camoesas Silva

Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal.

 

Laurentina Pedroso

Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal.Faculty of Veterinary Medicine, CECAV—Centre of Animal and Veterinary Science, Lusófona University, 1749-024 Lisbon, Portugal.

 

Ana Lima

Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal.Faculty of Veterinary Medicine, CECAV—Centre of Animal and Veterinary Science, Lusófona University, 1749-024 Lisbon, Portugal.

Please see the link :- https://doi.org/10.9734/bpi/rpmab/v3/8496E

Computational Approaches for Prediction of Conformational Epitopes for Birch Betv 1 and Hazel Cor A1 Targeting B-cells | Chapter 3 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 

Through targeted interactions mediated by receptors on antibodies, B-cells

effectively neutralize invading pathogens by binding with remarkable precision to

specific molecular regions, called epitopes. This study focuses on enhancing B

cell epitope predictions via computational methods. Antigen sequences are

fragmented into peptides and docked against IgE antibodies to identify top

scoring interactions. Peptides with the highest scores undergo further analysis to

assess bond interactions. By examining overlapping sequences within the

antigen model, the positions of predicted epitopes are determined. Residues

involved in bond interactions are documented for these overlapping peptide

sequences. Validation is achieved through antigen-antibody docking studies to

confirm the predicted epitope sites. Ultimately, the integration of computational

and experimental methodologies holds promise for the rational design of

immunotherapeutic interventions targeting Birch and Hazel allergens, paving the

way for precision medicine in allergy treatment. 

 

Author (s) Details

Praveen Kumar Vemuri
Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Green Fields, Vaddeswaram, Andhra Pradesh, India.

 

Varshitha Katta
Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Green Fields, Vaddeswaram, Andhra Pradesh, India.

Anupama Ammulu Manne
Department of Civil Engineering, PVP Siddhartha Institute of Technology, Kanuru, Vijayawada, Andhra Pradesh, India.

Kanaka Durga Devi Nelluri
KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh, India.

 Suryanarayana Veeravilli

Department of Humanities and Basic Sciences, Aditya University, Surampalem, Andhra Pradesh, India.

 KRS Sambasiva Rao

Department of Pharmacy, Mangalayatan University, Jabalpur, Madhya Pradesh, India.

Please see the link :-  https://doi.org/10.9734/bpi/rpmab/v3/187

Dermatophytosis: A Report from Tertiary Care Hospital in Davanagere, Karnataka, India | Chapter 4 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 

Background: Dermatophytosis refers to superficial fungal infection of keratinized  tissue caused by Dermatophytes. It is more prevalent in tropical and subtropical  countries including India where heat and moisture play an important role in  promoting the growth of these fungi. Dermatophytosis though not life threatening,  its severity should not be underestimated as it can cause great discomfort and at  times cause disability and disfigurement. So laboratory investigations are  important for correct diagnosis, management and minimizing cost.  Objective: The present study was undertaken to know the clinico-mycological  profile of dermatophytic infection, prevalence of various species, the co-relation  between the site of involvement and causative agent and to compare KOH smear  positivity with culture positivity.

Design: Prospective observational study.

Methods: Samples from total of 200 clinically diagnosed cases of  dermatophytosis were subjected to microscopy with 10%KOH, fungal culture on  SDA agar and further identification of the species based on standard tests. 

Results: Out of 200 cases, Tinea corporis 89 cases (44.5%) was the commonest

clinical presentation followed by Tinea cruris. The common species isolated was

Trichophyton rubrum 86(65.2%) followed by Trichophyton mentagrophytes

28(21.2%).

Conclusion: The present study gives valuable insight into the clinical and  mycological pattern of superficial fungal infections in this region as well as shows  the importance of mycological examination of dermatophytosis samples for  planning effective management.

 

Author (s) Details

G.K. Mangala

Department of Microbiology, J.J.M. Medical College, Davanagere - 577 004, India.

 

N.R. Chandrappa

Department of Microbiology, J.J.M. Medical College, Davanagere - 577 004, India.

 

V. Vijayanath
Department of Forensic Medicine & Toxicology, S.S. Institute of Medical Sciences & Research Centre, Davangere - 577 005, India.

 

Please see the link :-  https://doi.org/10.9734/bpi/rpmab/v3/265

Determination of Emitted Hydrogen (H2) from Bacterial Cultures in Closed Septum Vials by Gas Chromatography (GC) and Specific Hydrogen Sensor Techniques | Chapter 6 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 

The present study primarily focuses on the determination of emitted hydrogen

(H₂) from bacterial cultures in closed septum vials and both techniques, static-GC

as well as the sensor approach. When microorganisms are cultivated in suitable

nutrient medium in closed septum vials, their emission of hydrogen (H2) is

detected using a particular hydrogen sensor in addition to headspace-gas

chromatography. Facultative anaerobes are able to release both CO2 and H2

which are important chemicals for both types of bacteria, whereas obligatory

aerobic bacteria can only create CO2 and water through aerobic oxidation. 

Obligate anaerobic bacteria emit H2 too but need an oxygen-free atmosphere

which can be achieved if the air in the septum vial is replaced by nitrogen. The

samples under investigation, either solid or liquid samples and from smears by

wads from a cotton bud, are cultured in the headspace vials and the hydrogen

emission was monitored after the necessary time of incubation and thus microbe

contamination was detected. Antibiotics added to the bacterial culture in the vial

are found to be effective if any gas emission is suppressed. If not, they are either

ineffective or the bacteria are even resistant. Antibiotics, both synthetic and

natural, were investigated and some were discovered to be resistant or

ineffective. This technique was used to look into food contamination by bacteria,

household necessities, medical specimens, and Lyme borreliosis caused by tick

infection, as well as to diagnose and treat the disease. The borrelia bacteria that

cause infection are found in ticks and, later on, in human blood after they enter

the host. The foregoing examples show how essential oils can stop bacterial

infections in various samples but this method can also be applied in human

medicine and tick-borne Lyme disease is taken here as representative for

diagnosis and therapy of diseases caused by bacterial infections in humans. The

effect of the antibiotics applied can be examined and the progress of an antibiotic

therapy can be controlled until its final success is recognized.

 

Author (s) Details

Dr. Bruno Kolb

Student Research Centre, Überlingen, Obertorstrasse, Germany

 

Please see the link:-  https://doi.org/10.9734/bpi/rpmab/v3/370

Study of Spirometra Egg by Scanning Electron Microscopy: Operculum and Operculum Suture at one End | Chapter 2 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 Spirometra is a zoonotic parasite. An egg is the first stage in the life cycle of

Spirometra species. It can be used in the identification of Spirometra species.

Spirometra eggs were collected from the faeces of experimentally infected cats.

The eggs collected were used for morphological studies using light microscope

and scanning electron microscope (SEM). Eggs collected from faeces of cats

were fixed in 4% Glutaraldehyde, then post fixed in 1% Osmium tetroxide,

dehydrated in ethanol series. Dehydrated material was dried to a critical point

with carbon dioxide in a Polaron Critical Point Dry (CPD 7501). The dried

material was mounted on aluminium stubs. The specimen was gold-coated in a

sputter coater (B10-RAD). Then eggs were examined in a Philips SEM 515.

Scanning electron microscopy (SEM) images revealed the presence of

operculum and operculum suture at one end of the egg.

Author(s) Details

Nicholas Jairo Kavana

Department of Microbiology and Parasitology, Faculty of Medicine, St. Francis University College of

Health and Allied Sciences, Ifakara, Tanzania. 

 

Please see the link - https://doi.org/10.9734/bpi/rpmab/v3/3682G

Multidrug and Methicillin Resistant Staphylococcus aureus (MRSA) Isolated from Clinical Samples | Chapter 10 | Research Perspectives of Microbiology and Biotechnology Vol. 3

 

Aim: The present study aimed to detect inducible clindamycin resistance,

vancomycin resistance and mupirocin resistance among MRSA isolates.

Background: Multidrug and methicillin resistant Staphylococcus aureus is a

widely spread problem in clinical environment, therefore current information

regarding antimicrobial susceptibility of the pathogen is very important for the

treatment of patients and in control and prevention strategy. S. aureus, a

common pathogen, well known for its multidrug resistance. Existence of MRSA is

further worsened by inducible clindamycin resistance and emerging glycopeptide

resistance. 

Materials and Methods: The study was conducted for a period of 6 months from

May to October 2010. A total of 100 non-repetitive S. aureus isolates from

various clinical specimens were included in the study. A total of one hundred

non-repetitive isolates were subjected to routine antibiotic susceptibility testing by

Kirby Bauer’s disc diffusion method including cefoxitin disc for MRSA. Inducible

clindamycin resistance was detected by D-test, E-test for vancomycin MIC and

mupirocin resistance by disc diffusion.

Results: Twenty three (85.2%) isolates showed inducible clindamycin

resistance, one (3.7%) showed constitutive resistance and three (11.1%) showed

MS phenotypes. Inducible clindamycin resistance (35.7%), constitutive

resistance (2.3%) and MS phenotype (7.1%) were found to be higher in MRSA

as compared to MSSA. Only one isolate with vancomycin MIC 4µg/ml by E-test

was considered as VISA. In our study, only one strain, which had MIC 4µg/ml

has been considered as VISA. VISA may demonstrate heteroresistance or there

may be subpopulations that are resistant. Screening for hVISA requires

additional testing to reveal its hetero-variant phenotype and these methods are

more labor intensive and costly than routine susceptibility testing. Our study

detected mupirocin resistance in 11(26.1%) MRSA and 30(51.72%)MSSA

isolates, which is a cause for concern. Study showed that D-test should be

included as a routine disc diffusion test to prevent therapeutic failure with

clindamycin.

Author (s) Details

G.K. Mangala

Department of Microbiology, JJM Medical College, Davangere, Karnataka, India.

Ravindra. B

Department of Ophthalmology, JJM Medical College, Davangere, Karnataka, India.

K. Suresh

Department of Microbiology, JJM Medical College, Davangere, Karnataka, India.

Please see the link - https://doi.org/10.9734/bpi/rpmab/v3/266