Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities

Methodology for the analysis of biological impurities associated with peri-eucharistic phenomena

One of the central dogmas of the Catholic Church is the belief in the Eucharistic presence of Jesus Christ, which requires no scientific confirmation because it concerns a supernatural reality. Since the early Middle Ages, however, instances have been recorded improperly referred to as Eucharistic miracles, which believers consider eyewitness testimony to a real transubstantiation. Changes in the structure, number, or an unexpected bloody red colour of the Host were often regarded as supernatural phenomena, but the Church officials themselves, aware of the possibility of a biological basis for these changes, showed far-reaching restraint. The author's team on the basis of analyses of 25 actual cases undertook to prepare research procedures that make it possible to separate phenomena that are difficult to interpret scientifically, from those associated with contamination. None of these cases revealed the actual proof of existence of human blood, human material other than single epidermal cells, and erythrocytes (probably very low-level contamination). In one case, insignificant amount of human male genetic material was observed, probably as a result of DNA transferred from a person to a host via contact with the host itself. In several specimens, a variety of microbial and fungal material was identified (Brevundimonas intermedia, Serratia marcescens, Epicoccum spp,. Fusarium spp.), including species producing reddish-pink or orange-reddish pigments (Epicoccum spp., Fusarium spp.). Based on the experience gained in this study, a complete procedure suitable for reliable examination of similar cases in the future is suggested. KEY POINTS: • The unusual appearance of the tested hosts can be explained by biological contamination. • Blood-like marks result from the presence of pigment-producing species. • A complete multidisciplinary procedure for investigating 'miracle cases' is proposed.

MetaBIDx: a new computational approach to bacteria identification in microbiomes

Objectives: This study introduces MetaBIDx, a computational method designed to enhance species prediction in metagenomic environments. The method addresses the challenge of accurate species identification in complex microbiomes, which is due to the large number of generated reads and the ever-expanding number of bacterial genomes. Bacterial identification is essential for disease diagnosis and tracing outbreaks associated with microbial infections. Methods: MetaBIDx utilizes a modified Bloom filter for efficient indexing of reference genomes and incorporates a novel strategy for reducing false positives by clustering species based on their genomic coverages by identified reads. The approach was evaluated and compared with several well-established tools across various datasets. Precision, recall, and F1-score were used to quantify the accuracy of species prediction. Results: MetaBIDx demonstrated superior performance compared to other tools, especially in terms of precision and F1-score. The application of clustering based on approximate coverages significantly improved precision in species identification, effectively minimizing false positives. We further demonstrated that other methods can also benefit from our approach to removing false positives by clustering species based on approximate coverages. Conclusion: With a novel approach to reducing false positives and the effective use of a modified Bloom filter to index species, MetaBIDx represents an advancement in metagenomic analysis. The findings suggest that the proposed approach could also benefit other metagenomic tools, indicating its potential for broader application in the field. The study lays the groundwork for future improvements in computational efficiency and the expansion of microbial databases.

Isolation and Characterization of Aeromonas jandaei from Nile Tilapia in Lake Volta, Ghana, and Its Response to Antibiotics and Herbal Extracts

Production of Nile Tilapia Oreochromis niloticus contributes to economic growth in many countries. However, there has been a decline in its production over the years due to the influx of bacterial infections, with Aeromonas jandaei as an emerging threat. In this study, we identified and characterized A. jandaei from cage-cultured Nile Tilapia in Akosombo Stratum II of Lake Volta in Ghana and evaluated its response to commonly used antibiotics using the disc diffusion and agar well diffusion methods for herbal extracts at various concentrations (10, 30, 50, 70, and 100 mg/mL). The herbs considered included guava Psidium guajava leaf, bitter leaf Vernonia amygdalina, neem Azadirachta indica leaf, and their cocktail (GBNL in the ratio of 1:1:1). The bacterium was isolated from swab samples from the head kidneys of 27 moribund Nile Tilapia collected from nine fish farms. Samples were screened for A. jandaei by culturing and identification using morphological and molecular techniques. The bacterium isolate from fish in the study, identified as A. jandaei GH-AS II, had 92-93% identity to A. jandaei reference strains. Infection of healthy Nile Tilapia (n = 210) with the bacterium isolate showed that 1.0 × 10⁵  CFU/mL was the lethal dose causing 50% mortality. Antibiotic susceptibility testing showed that A. jandaei GH-AS II was resistant to tetracycline and ampicillin. Herbal extracts at the various concentrations inhibited the growth of the bacterium isolate, with a significant increment in the zones of inhibition with increasing concentrations of leaf extracts. However, GBNL showed prominence compared to the other extracts only at 100 mg/mL. Management of A. jandaei GH-AS II by using herbal extracts at Nile Tilapia farms in Lake Volta may be recommended since the use of antibiotics, such as tetracycline and ampicillin, may not yield the needed result.

A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.

Comparison of Clinical Characteristics for Distinguishing COVID-19 From Influenza During the Early Stages in Guangdong, China

Background: To explore the differences in clinical manifestations and infection marker determination for early diagnosis of coronavirus disease-2019 (COVID-19) and influenza (A and B).

Methods: A hospital-based retrospective cohort study was designed. Patients with COVID-19 and inpatients with influenza at a sentinel surveillance hospital were recruited. Demographic data, medical history, laboratory findings, and radiographic characteristics were summarized and compared between the two groups. The chi-square test or Fisher's exact test was used for categorical variables, and Kruskal–Wallis H-test was used for continuous variables in each group. Receiver operating characteristic curve (ROC) was used to differentiate the intergroup characteristics. The Cox proportional hazards model was used to analyze the predisposing factors.

Results: About 23 patients with COVID-19 and 74 patients with influenza were included in this study. Patients with influenza exhibited more symptoms of cough and sputum production than COVID-19 (p < 0.05). CT showed that consolidation and pleural effusion were more common in influenza than COVID-19 (p < 0.05). Subgroup analysis showed that patients with influenza had high values of infection and coagulation function markers, but low values of blood routine and biochemical test markers than patients with COVID-19 (mild or moderate groups) (p < 0.05). In patients with COVID-19, the ROC analysis showed positive predictions of albumin and hematocrit, but negative predictions of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), hydroxybutyrate dehydrogenase (HBDH), and erythrocyte sedimentation rate. Multivariate analysis revealed that influenza might associate with risk of elevated CRP, PCT, and LDH, whereas COVID-19 might associated with high HBDH.

Conclusion: Patients with influenza had more obvious clinical symptoms but less common consolidation lesions and pleural effusion than those with COVID-19. These findings suggested that influenza likely presents with stronger inflammatory reactions than COVID-19, which provides some insights into the pathogenesis of these two contagious respiratory illnesses.

Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.

Oral microbiome: Unveiling the fundamentals

The oral cavity has the second largest and diverse microbiota after the gut harboring over 700 species of bacteria. It nurtures numerous microorganisms which include bacteria, fungi, viruses and protozoa. The mouth with its various niches is an exceptionally complex habitat where microbes colonize the hard surfaces of the teeth and the soft tissues of the oral mucosa. In addition to being the initiation point of digestion, the oral microbiome is crucial in maintaining oral as well as systemic health. Because of the ease of sample collection, it has become the most well-studied microbiome till date. Previously, studying the microbiome was limited to the conventional culture-dependent techniques, but the abundant microflora present in the oral cavity could not be cultured. Hence, studying the microbiome was difficult. The emergence of new genomic technologies including next-generation sequencing and bioinformatics has revealed the complexities of the oral microbiome. It has provided a powerful means of studying the microbiome. Understanding the oral microbiome in health and disease will give further directions to explore the functional and metabolic alterations associated with the diseased states and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine. This review article is an attempt to explain the different aspects of the oral microbiome in health.

Oral microbiome: Unveiling the fundamentals

The oral cavity has the second largest and diverse microbiota after the gut harboring over 700 species of bacteria. It nurtures numerous microorganisms which include bacteria, fungi, viruses and protozoa. The mouth with its various niches is an exceptionally complex habitat where microbes colonize the hard surfaces of the teeth and the soft tissues of the oral mucosa. In addition to being the initiation point of digestion, the oral microbiome is crucial in maintaining oral as well as systemic health. Because of the ease of sample collection, it has become the most well-studied microbiome till date. Previously, studying the microbiome was limited to the conventional culture-dependent techniques, but the abundant microflora present in the oral cavity could not be cultured. Hence, studying the microbiome was difficult. The emergence of new genomic technologies including next-generation sequencing and bioinformatics has revealed the complexities of the oral microbiome. It has provided a powerful means of studying the microbiome. Understanding the oral microbiome in health and disease will give further directions to explore the functional and metabolic alterations associated with the diseased states and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine. This review article is an attempt to explain the different aspects of the oral microbiome in health.

Genetic diversity of symbiotic bacteria nodulating common bean (Phaseolus vulgaris) in western Kenya

Biological nitrogen fixation (BNF) in legumes plays a critical role in improving soil fertility. Despite this vital role, there is limited information on the genetic diversity and BNF of bacteria nodulating common bean (Phaseolus vulgaris L.). This study evaluated the genetic diversity and symbiotic nitrogen fixation of bacteria nodulating common bean in soils of Western Kenya. The genetic diversity was determined using 16S rRNA gene partial sequences while BNF was estimated in a greenhouse experiment. The sequences of the native isolates were closely affiliated with members from the genera Pantoea, Klebsiella, Rhizobium, Enterobacter and Bacillus. These results show that apart from rhizobia, there are non-rhizobial strains in the nodules of common bean. The symbiotic efficiency (SE) of native isolates varied and exhibited comparable or superior BNF compared to the local commercial inoculants (CIAT 899 and Strain 446). Isolates (MMUST 003 [KP027691], MMUST 004 [KP027687], MMUST 005 [KP027688], KSM 001 [KP027682], KSM 002 [KP027680], KSM 003 [KP027683] and KSM 005 [KP027685]) recorded equal or significantly higher SE (p < 0.05) compared to N supplemented treatments. The results demonstrate the presence of genetic diversity of native bacteria nodulating bean that are effective in N fixation. These elite bacterial strains should be exploited as candidates for the development of Phaseolus vulgaris inoculants.