Innovations in Microbiology and Biotechnology Vol. 2

Water is a precious and dwindling resource. The enormous increase in domestic and industrial water consumption has been accompanied by a commensurate increase in the production of domestic and industrial effluents. Despite the limited availability of water, seas, rivers and lakes have been used as sinks for the disposal of domestic and industrial wastewater. Various effluent treatment methods have been developed to clean effluents and enable their reuse as efforts to conserve water.

Some pollutants in wastewater persist in the environment because they are resistant to degradation by conventional treatment methods. The present chapter attempts to explore the use of enzymes as an alternative method for degrading recalcitrant pollutants in wastewater. The aim of the present chapter is to provide an account of various delivery systems that can be used to introduce enzymes into the reaction mixture during wastewater treatment. The chapter discusses different modes, such as the use of microbial or plant cells, cell-free extracts, and nanoparticles, by which enzymes can be delivered to degrade target pollutants in effluents, and it assesses the strengths and drawbacks of each mode. Furthermore, the need for current and future research to prioritize the development of economically feasible and environmentally sustainable wastewater treatment practices is emphasized.

In herbal medicine, crude plant extracts in the form of herbal extracts are used by the population for the treatment of diseases, including infectious diseases. Several hundred genera of plants are used as vital sources for potent and powerful drugs. The objective of present study were to determine the antimicrobial effect of some natural products of herbal and spice extracts; and compare the antimicrobial activity these aqueous and ethanolic extract test products with reference to MIC and MBC. The current study was carried out on five selected fresh samples from various conditions. Using the agar well and disc diffusion methods, the antimicrobial effects of Tripfala, Java plum, Cinnamon, Henna, and Cumin against both gram-positive and gram-negative bacteria were investigated. The zone of inhibition or antimicrobial activity of aqueous extracts of selected sample extracts was greater than that of ethanolic extracts. Among the five selected microbes, Klebsiella sp. had the lowest sensitivities to Tripfala and Java plum extracts, whereas these aqueous and ethanolic extracts had strong antimicrobial activity against four other microbes. The MIC values for all of the natural products ranged from 12.5-25.0 ug/ml, while the MBC values ranged from 25- 100.0ug/ml. During the four-month preservation of prepared discs of these natural plant products, no change in antimicrobial activity was observed. This research suggests that Tripfala and Java Plum have the potential to be used as a source of new broad-spectrum oral antibiotics.

Objectives: Emergence of clinical isolates with extended spectrum beta lactamase (ESBL) producing capabilities has created therapeutic challenges. Thus, ESBLs are of increasing clinical concern in worldwide as confers resistance to broad spectrum \(\beta\)-lactam antibiotics. Because neonates are more prone to infections, it is a major concern chiefly in Neonatal Intensive Care Units (NICUs). It is responsible for therapeutic failure and neonatal mortality when neonates are treated with cephalosporins; hence its detection and knowledge of present scenario of prevalence is crucial for infection control. The present study explored the incidences of ESBL producers among infectious neonates included under the study.

Materials and Methods: 1611 suspected cases of neonatal infections were included under study during 25 months (December 2010 to January 2013). Among 342 positive cases, 211 were identified as gram negative by strict microbiological standards and were checked for ESBLs productions. Double disc diffusion test was used for suspection of ESBL production and were further confirmed by the double disc synergy test (DDST) and the phenotypic confirmatory disc diffusion test (PCDDT).

Results: Out of the 212 isolates, 39.34% screened as prospective ESBLs producers. 29.39%   were confirmed by DDST and 27.97% by PCDDT. Escherichia coli were the most common ESBL producers found followed by K. pneumoniae. Finally, high prevalence of ESBL producers in N.I.C.Us., knocking the essentiality of detection of ESBL production routinely with sensitivity reports that may guide neonatologist to accomplish the therapeutic challenge 

Emerging and re-emerging infectious diseases have had a negative impact on the world. Fighting these diseases claimed the lives of nearly 14 million people. These emerging infectious diseases have the potential to cause epidemics and pandemics. History itself has shown that viruses cause a lot of pandemics and caused a lot of destruction.  These infectious agents will always be after humans to cause diseases.  We can, however, thwart them with scientific techniques. WHO proposed the names of ten potential viruses that could cause the next outbreak and pandemic in 2015. All of these viruses have occurred in the last two decades and have caused widespread devastation. Some are still infecting humans.  In order to detect and respond to these infectious agents, surveillance is critical. The use of molecular technologies, phylogenetic and phylogeographic analysis has demonstrated that we can prevent outbreaks by forecasting them. Genomic epidemiology is being used for the development of interventions and limiting the spread of these infectious diseases. A response strategy has been proposed to affected countries by the World Health Organization and the Global Outbreak Alert and Response Network. In the event of an emergency outbreak, the GOARN team must arrive in those countries within 24 hours. There are some control measures in place to prevent the spread of existing outbreaks as well as the occurrence of future outbreaks. This paper aims to convey the significance of awareness and vigilance to the readers so that they can contribute their part in preventing outbreaks. 

Clostridium difficile is an important emerging infectious agent, and might colonize in digestive tract of animals and humans. C. difficile exhibits a low level of gene conservation. Consequently, antibiotic therapy has demonstrated in 15-30% effectiveness of the cases. In the current review we summarized up to date information about the drug resistance genotypes of C. difficile for the first time, including sporulation and motility methods, growth suitability, antibiotic susceptibility, and whole-genome sequencing. PCR enables to certify the recurrences were a mixture of original (relapse) and new strains (reinfection). Our study revealed that there was a steady difference among various genotypes, demonstrating that mutations in the DNA genes were common in the antibiotic resistance phenotypes. Together our data revealed that antibiotic resistance poses selective pressure on the genome evolution of C. difficile that could lead to more adoptable strains with drug resistance. This study may open a new avenue for the research in understanding the mechanism of C. difficile adaptation to antibiotics and development of new antibacterial drugs. However, further research is needed to explore C. difficile genomic diversity changed from molecular typing assays to total-genome sequence comparisons, and comparative genome microarrays.

Endophytic bacterial diversity in maize (Zea mays L.) cultivated on Acrisols of the Southeast of Vietnam was studied. Twenty-eight maize stem and root samples were collected from five sites (provinces/cities) of this region. Endophytic bacteria were isolated in two kinds of media (LGI, NFb) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 301 isolates were isolated and all of them had ability of nitrogen fixation and phosphate solubilization along with IAA biosynthesis but there were 30 isolates having the best characteristics and they were identified as maize endophytes and nifH gene owners. The sequences from selected endophytic bacteria (30 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). Among the selected isolates, 6 isolates belonged to Bacillus (20.00%) and 24 isolates belonged to Proteobacteria (80.00%) including 2 alpha-proteobacteria (7%), 6 beta-proteobacteria (20%), and 16 gamma-proteobacteria (53%). Based on Pi value (nucleotide diversity), Proteobacteria group had the highest Theta values and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Proteobacteria group had the highest values in comparison of two groups. From these results showed that 3 isolates including DTN1b (Azotobacter vinelandii), VTN2b (Bacillus subtilis) and VTN7 (Enterobacter cloacae) proposed as potential microbial inoculants or biofertilizers for sustainable corn production in poor Acrisols in Vietnam because of their benefit and biosafety.

We had the beneficial bacteria for wastewater treatment, the next step was heterotrophic nitrogen removal in Pangasius fish’ (TRA) ponds in the Mekong Delta. A total of 2318 heterotrophic nitrogen removal (HNR) bacteria isolated from piggery wastes (after biogas container) were classified in four kinds of heterotrophic ammonia-oxidizing bacteria (569 isolates), nitrite-oxidizing bacteria (580 isolates), nitrate-oxidizing bacteria (600 isolates) and heterotrophic nitrifying and denitrifying bacteria (569 isolates). The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the selected HNR bacteria showed high degrees of similarity to those of the GenBank references strains (between 97% and 99.8%). Phylogenetic trees based on the 16S rDNA sequences displayed high consistency, with nodes supported by high bootstrap (500) values. These presumptive HNR isolates were divided four groups that included members of genera Arthrobacter, Corynebacterium, Rhodococcus (high G+C content gram-positive bacteria), Staphylococcus, Bacillus (low G+C content gram-positive bacteria) and Klebsiella (gram-negative bacteria). Based on Pi value (nucleotide diversity), heterotrophic ammonium-oxidizing bacteria group had highest values and heterotrophic nitrifying-denitrifying bacteria group had the lowest values and Theta values (per sequence) from S of SNP for DNA polymorphism showed that heterotrophic nitrate-oxidizing bacteria group had the highest theta values in comparison of three groups. The present study, the HNR bacteria from piggery wastes, showed a very diverse community of HNR bacteria with a relatively high number of species involved in solid-wastewater samples and many isolates have nitrogen utilization ability at high concentration (800 – 1200 mM) and high G+C gram-positive bacteria strain occupied higher than low G+C gram-positive bacteria strain.

Aims: The work investigated the effects of plant seeds such as fenugreek (Trigonella foenum-  graecum L.), wheat grains (Triticum aestivum L.), and hot red pepper (Capsicum annuum L.) which are traditionally used as natural food preservatives or at least to minimize the used concentrations of artificial preservatives, meantime to serve as antibacterial agents against certain positive and negative gram bacteria such as Staphylococcus aureus ATCC 29213 and Enterobacter cloacae  Enk1 LT592256 and the effectiveness of using germinated seeds in reducing bacterial growth.

Study Design: The experiments were designed as one way completely randomized design.

Place and Duration of Study: The experiments were carried out at the Regional Center for Food and Feed (RCFF), Agricultural Research Center, and Faculty of Agriculture Saba Basha, Alexandria University, Egypt.

Methodology: The living bacterial cells in each treatment was estimated after 5 days of incubation at 25°C the total viable bacterial counts were determined using the plate count agar method. Microbial numbers in all samples were determined using serial dilutions also, determine the total flavonoids, antioxidant activity, and total phenol contents of the tested seeds and their germs.

Results: Our results demonstrated that the maximum number of S. aureus bacteria in 10^-1 on wheat germinated seeds extract at 1000 µl that is 290 CFU and the maximum number of E. cloaceae was 370 CFU was found in wheat non-germinated seeds at 500µl concentration, however, the highly inhibitory concentration of S. aureus 1000 µl was realized using non-germinated red pepper seeds extract (97.9%) and (92.9%) in the case of E. cloaceae bacteria. The maximum inhibition percentage was found with red pepper non-germinated seeds for (S. aureus) it was (97.9%) and for the (E. cloaceae) was (92.9%) under the concentration 1000 µl. The results showed that germs extract was less effective as an antibacterial agent than seed extract. S. aureus was more susceptible than E. cloacae. The use of hot red pepper seeds extracts then fenugreek extract was highly effective in reducing the growth of both the tested bacteria.

Conclusion: Food spoilage is frequently caused by the proliferation of many pathogenic bacterial strains. Food spoilage prevention in the food industry and food stuff is primarily based on the use of chemical preservatives. Hot pepper and fenugreek extracts can be used as natural alternative preventives to control food poisoning diseases. Non Germinated seeds are most effective against studied bacteria growth.

The use of nanotechnology in biological fields have gained tremendous attention in recent times with their application in fields like cancer therapy, drug delivery, biosensors, antioxidant, anti-microbial, agriculture etc. Gold, silver, iron, copper, nickel and selenium for their excellent biological activity are the most commonly synthesized nanoparticles, of which selenium nanoparticles will be the main focus of this review. Green synthesis of SeNPs is an environmentally safer option than other methods. Based on the raw materials and the techniques used, selenium nanoparticles of various shapes and sizes can be fabricated which imparts specific properties to each form of nanoparticles produced. Plant samples such as Aloe vera leaves, citrus fruits and cinnamon bark having known bio-active properties are found suitable for green synthesis of selenium nanoparticles. The advantages of using selenium are its availability in nature, lower toxicity (in its nanoparticle form) and its antimicrobial and antioxidant properties. The combined effect of the plant's bioactive properties, selenium's antioxidant properties and increased reactivity in nano-particle form have worked wonders against some of the harmful human pathogens even though the exact mode of action is not known. With the growing resistance of microbial pathogens against the current arsenal of antibiotics, these modern approaches are the need of the highest order in our fight against microbial infections. Here in this review, green synthesis of Selenium nanoparticles using different plant extracts, their characterization techniques and the antimicrobial activity against several bacteria and fungi have been discussed.

The objective of present study was to observe biological activities and comparison of the isolated ayurvedic and unani medicine. All of the ayurvedic medicines were more effective antimicrobial agents than unani medicine against all of the tested organisms in in vitro culture condition. Mustakarista showed highest zone of inhibition against Staphylococcus sp. in concentration at neat and 1:2. Highest MIC was found in Amritarista against Mycobacterium sp. and highest MBC were observed against Staphylococcus sp.; in Mustakarishta, highest MIC against Klebsiella sp. and highest MBC was observed against Mycobacterium sp.; in Ashokarista, highest MIC against Vibrio cholera and highest MBC was observed against Staphylococcus sp.; in Amalaki Rasayan, highest MIC against Salmonella sp. and highest MBC were observed against Escherichia coli, Staphylococcus sp. and Bacillus subtilis. Combined effect of test product against selected microbes showed satisfactory results against all the selected microbes. All ayurvedic medicines have nearly twice the antimicrobial activity of unani medicine, whereas most commercial antibiotics have only a minor response against all tested organisms.