Open Access Original Research Article

Scardovia wiggsiae and Streptococcus sobrinus Prevalence among Orthodontic and Non-Orthodontic Patients

Melissa Trumbo, Namgu Kim, Beanca Jhanine Samiano, Matthew Marrujo, Patrick Perkins, Kevin Foote, Katherine M. Howard, Karl Kingsley

Microbiology Research Journal International, Page 1-12
DOI: 10.9734/mrji/2021/v31i230292

Background: Dental cavities or caries have been identified as among the most prevalent of preventable oral conditions. However, studies are discovering new information regarding the incidence and prevalence of several cariogenic organisms, including Streptococcus mutans (SM), the recently discovered Scardovia wiggsiae (SW), as well as Streptococcus sobrinus (SS). These studies have revealed varying prevalence among different populations, such as those undergoing orthodontic treatment. Based upon this information, the main goal of the current study was to assess the prevalence of specific cariogenic organisms (SS and SW) within saliva samples originally obtained from a dental school-based clinic.

Methods: The protocol for this retrospective study of DNA isolated from previously collected saliva samples was reviewed and approved by the Institutional Review Board (IRB) as exempt research. In brief, clinical DNA samples were screened for SS and SW using quantitative polymerase chain reaction (qPCR). Demographic and subgroup (Orthodontic, non-Orthodontic) analysis was also performed.

Results: This study found that pediatric (12-17 year old patient) samples were much more likely to harbor either SW or SS compared with adult (>18 year old patient) samples. In addition, this study found many more SW-positive samples among pediatric orthodontic patients compared with either adult or pediatric non-Orthodontic patients, which may suggest this population may be at higher risk for SW-related caries or other negative oral health outcomes. Finally, this study found these microbial populations to be strongly linked within the same patient samples.

Conclusions: This study has demonstrated that prevalence of SW and SS may be more highly associated with specific population subgroups, including SS observed in non-orthodontic patients and SW found among pediatric orthodontic patients. These results also differ from previous evidence, which found only minor and partially overlapping prevalence of these and other oral microbes.  The results of this current study may suggest that SS and SW may be more strongly correlated within similar oral microbial communities and their presence may be directly or indirectly linked through one or more behavioral, microbial or other factors – although more research will be needed to determine these mechanisms.

Open Access Original Research Article

Strain-level Identification of Beneficial Lactobacilli of Dairy Origin using 16S rRNA Sequencing: A Biotechnology Approach

S. Aforijiku, C. O. Fakorede, A. B. Adediran

Microbiology Research Journal International, Page 13-21
DOI: 10.9734/mrji/2021/v31i230293

Aim: This study investigated the cultural method and 16S rRNA gene analysis to reveal the composition and diversity of lactic acid bacteria (LAB) from dairy origin (spontaneous fermented cow milk) in Nigeria.

Methods: Six dairy samples which includes two raw cow milk, two raw goat milk and two fermented cow milk (nono) were collected and subjected to standard microbiological investigation using both cultural and molecular methods. The dairy samples were cultured on MRS media, and the isolates were identified using physiological and biochemical parameters. DNA of four selected probiotic LAB isolates from nono were amplified using PCR while the amplicons were electrophoresed in agarose gel, pre-stained with ethidium bromide and characterized by 16S rRNA gene analysis. The result of the DNA sequencing were analyzed using NCBI BLAST. 

Results: A total of 55 presumptive LAB were isolated. Twenty nine (29) Lactobacillus plantarum representing 52.7%, Pediococcus acidilactici 15(27.2%), Lactobacillus casei and Lactobacillus brevis 4(7.3%) while Lactobacillus fermentum 3(5.5%) were recorded respectively. Result of the gel electrophoresis revealed DNA size of approximately 1500bp. The selected probiotic LAB from nono used in this study were confirmed as Lactobacillus plantarum N17, Lactobacillus plantarum N24, Lactobacillus brevis N10 and Lactobacillus casei N1 based on 16S rRNA gene sequence analysis while the phylogenetic analysis revealed a 98-100% similarity with a high homology level which affirms the strain of the organism.

Conclusion: This study has demonstrated the diversity of LAB existing in dairy samples known as fermented cow milk (nono) which could be harnessed as valuable sources for LAB isolation and potential probiotic organisms.

Open Access Original Research Article

Characterisation of Some Selected Bacterial Isolates from Vegetable Oil Contaminated Soil

B. M. Popoola, A. A. Olanbiwoninu

Microbiology Research Journal International, Page 22-37
DOI: 10.9734/mrji/2021/v31i230294

Microbial lipases occupy a place of prominence among biocatalysts and are often used for various biotechnological applications. Because of huge variation in applications, the availability of lipases with specific characteristics is still a limiting factor. There is therefore need for extensive characterisation of lipase for various applications. This work was carried out to characterise lipases from some selected bacterial isolates.

Isolates identified as Bacillus subtilis, Bacillus licheniformis, Pseudomonas cepacia Pseudomonas fluorescens, Alcaligenes sp. and Flavobacterium sp. from a vegetable oil contaminated soil were characterized. Temperature, pH and ion concentration, (NaNO3 and MgSO4), incubation time, agitation speed, carbon sources and nitrogen sources were optimised for growth and lipase activity. Increase in microbial growth does not necessarily suggest increase in lipolytic activity as generally observed from this study.  Temperature, pH, incubation time and agitation speed which had optimum enzyme activities for crude enzyme of Pseudomonas fluorescens (0.8 U/mL), were 27 oC, 7.0, 24 h, and 0 rpm respectively. Growth was not generally supported by AgN03 in all the organisms selected but supported by KNO3. However MgSO4 generally supported lipase production. Olive oil and peptone as sources of carbon and nitrogen respectively supported both growth and lipase production in the selected organisms.

These bacterial isolates characterized had lipolytic activities, hence they have high potential for various biotechnological applications.

Open Access Original Research Article

Optimal Conditions for Expression of Enzymatic Activities in Bacillus Strains Essential for Production of Soumbara, a Functional Fermented Food Involved in Blood Pressure Homeostasis

Yves A. Kouakou, Honoré G. Ouattara, Germain T. Karou

Microbiology Research Journal International, Page 38-52
DOI: 10.9734/mrji/2021/v31i230295

Background: Soumbara is a traditional fermented food involved in the blood pressure homeostasis. The functional properties of this food strongly depend on the fermentative microbiota. In this study, we screened and identified at molecular level, some potential starters strain among the main microbiota associated with soumbara in Cote d’Ivoire, and investigated the conditions for optimal expression of their functional performance.

Methods: We screened and identified by ribosomal gene sequencing, interesting microbial strains and conditions for optimal expression of their functional performance notably proteolytic, lipolytic, pectinolytic, amylolytic and cellulolytic activities was investigated using semi quantitative method.

Results: The isolated microbiota was composed of 90.41 % of Bacillus strains, the rest being yeast and lactic acid bacteria. A total of 4 performant strains, specifically Bacillus subtilis (BS14P), Bacillus subtilis (KS16P), Bacillus velezensis (HS27M) and Bacillus pumilis (PS10P) were extracellular enzymes producing strains with halo diameter ranging between 1.9 and 2.8 cm. These strains grew optimally in the temperature range of 30- 35°C at pH 7-8. The largest enzyme producer Bacillus velezensis strain (HS27M) was remarkably able to grow well at relatively high temperature (40°C) and in a larger pH range (6-9). Proteolysis enzymes were produced optimally at 40-45°C, pH 7 whereas lipolysis occurred maximally at 40°C, pH 7. Likewise maximum pectinolytis, cellulolysis and amylolysis occurred at 45°C, pH range 7-8.

Conclusion: This study suggests Bacillus velezensis HS27M as valuable starter cultures for the production of soumbara with bioactive and organoleptic quality.

Open Access Original Research Article

Microbiology and Heavy Metal Content of Wetlands Impacted by Crude Oil Pollution in Rivers State, Southern Nigeria

Mebom Princess CHIBUIKE, David N. OGBONNA, Janet Olufunmilayo WILLIAMS

Microbiology Research Journal International, Page 53-63
DOI: 10.9734/mrji/2021/v31i230296

Wetland soils constitute vast, under-exploited and sometimes undiscovered ecologies in many countries of the World, including Nigeria. A total of 54 wetland soil samples including surface and subsurface soil at depths of 0-15 cm and 15-30 cm were collected using a sterile hand auger for a period of three months between August and October and subjected to standard and analytical microbiological procedures. The wetland soil samples were further subjected to atomic absorption spectroscopy (AAS) to check for presence and concentration of heavy metals. Results obtained showed that apart from heterotrophic bacterial and fungal counts, hydrocarbon utilizing bacteria (HUB) counts were higher in the surface soil ranging from 12.06±3.43bX107 cfu/g at Iwofe to 6.19±2.67aX107 cfu/g at Chokocho while subsurface soil had HUB ranging from 8.91±6.67aX103 cfu/g at Eagle Island to 4.93±3.95aX103cfu/g at Chokocho. Heavy metals such as Fe, Pb, Cd and Ni were recorded in concentrations above FEPA permissible limit in the surface and subsurface soil across the three wetlands. The heavy metal concentration in each wetland however, decreased with an increase in soil depth. According to literatures, elevated levels of heavy metals in soils decrease microbial population, diversity and activities. However, the microbial population in this study increased with increasing heavy metal concentration which indicates that the microbes can tolerate or utilize heavy metals in their systems; as such can be used for bioremediation of heavy metal polluted soils. 

Open Access Original Research Article

Comparative Analyses of ACE2 Receptor Binding Corona Viruses that Cause Mild versus Severe Acute Respiratory Syndrome in Humans

Peramachi Palanivelu

Microbiology Research Journal International, Page 64-85
DOI: 10.9734/mrji/2021/v31i230299

Aim: To analyze the spike proteins and Replication-Transcription Complexes (RTCs) of the Mild and Severe Acute Respiratory Syndrome (SARS) and SARS-related coronaviruses (CoVs) to find out the similarities and differences between them, as both of groups bind to angiotensin-converting enzyme 2 (ACE2) receptor for human cell entry.

Study Design: Bioinformatics, Biochemical, Site-Directed Mutagenesis (SDM), X-ray crystallographic, cryo-Electron microscopic (cryo-EM) and Mass Spectrometric (MS) data were analyzed.

Methodology: The protein sequence data for spike proteins and the proteins of the RTCs, viz. the RNA- dependent RNA polymerases (RdRps), primases and the nonstructural protein 7 (NSP7) were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical and SDM experiments and X-ray crystallographic and cryo-EM  studies on these  proteins were used to confirm the possible amino acids involved in ACE2 receptor binding and active sites of the RTCs. For identification of probable N-linked and O-linked glycosylation sites, NetNGlyc 1.0 and NetOGlyc 4.0 tools of Technical University of Denmark were used. ExPASy tool was used for pI analysis.

Results: The spike protein of human CoV (HCoV)-NL63 is ~90 amino acids longer than the spike proteins of SARS and SARS-related CoVs. The additions are mostly found in the N-terminal regions and few insertions are also found in the crucial receptor binding domain (RBD). The SARS and SARS-related CoVs and HCoV-NL63 showed several conserved residues, motifs and large peptide regions. The most important aspect between the recent pandemic causing SARS-CoV-2 and HCoV-NL63 is a unique but different tetrapeptide insertions very close to the S1/S2 cleavage region, i.e., -PRRA-  and  -IPVR-, respectively. The next cleavage point S2’ and the transmembrane domains are conserved between the two groups. The RdRps are highly conserved between the two groups. The catalytic regions, catalytic amino acids and the NTP selection tripeptide regions are completely conserved between SARS-CoVs and HCoV-NL63.  However, one of the metal binding sites, viz. the universal –GDD- reported in all RdRps is aligning with– KDG- in the RdRp of HCoV-NL63. The other metal binding site, viz. –SDD- is completely conserved in both the groups. The NiRAN domains of the RdRps differed from the possible catalytic amino acid and NTP selection tripeptide regions. The primases (NSP8) and the NSP7 subunits of the RTC are highly conserved in both the groups. The NSP8 and NSP7 subunits exhibit closer similarities between the MERS-CoV and HCoV-NL63. Unlike other SARS and SARS-related CoVs, the HCoV-NL63 possesses only a single accessory protein. Interestingly, a large number of amino acids are replaced with Ns in the spike proteins (which is also reflected in the number of N-linked glycosylation sites in it) as well as in the RTC.

Conclusions: Detailed analysis revealed several unique features in the HCoV-NL63 pathogen. As all the pandemic strains like SARS-CoV-1, SARS-CoV-2 and the milder HCoV-NL63 strain, use the same ACE2 receptor for entry into human cells, the frequent infection of humans by HCoV-NL63, especially in children, suggests that there is an ample opportunity for highly pathogenic variants to evolve in the future.

Open Access Original Research Article

Influence of Cropping Practices on the Persistence and Vertical Migration of Escherichia coli from Wastewater in Hydromorph Soil in Wet Tropical Zone

Ntangmo Tsafack Honorine, Temgoua Emile, Kenfack Siméon, Njine Thomas

Microbiology Research Journal International, Page 86-97
DOI: 10.9734/mrji/2021/v31i230300

Little attention is paid to the influence of cultivation practices on the persistence and vertical migration of undesirable bacteria in hydromorphic soils as they have increased the risk of crop recontamination. Therefore the objective of this study was to determine the implication of some cultural practices on the persistence and vertical migration of E. coli in the soil. In this study, raw sewage (single application) and stream water (multiple application) were applied on lettuce, carrot and aubergine plots. The results revealed that overall, E. coli persisted longer on plots with crops and were more persisted in the rainy season on all cultivated plots that had received wastewater from the sewage treatment plant until harvest. While in the dry season, it was only detected at harvest on lettuce plots. The E. coli rate increased gradually overtime on the plots that had received water from the watercourse. Aubergine was the only plant that significantly facilitates the vertical migration of E. coli to the water table. On the whole, crops favored the persistence of E. coli on the soil surface and therefore increase the health risk related to the use of wastewater in agriculture.