Mutation of Bacillus velezensis Using Corona Discharge

Bacillus velezensis is a kind of beneficial bacteria that is widely used in agriculture industry. Bacillus velezensis was irradiated with corona discharge generated by a needle-array high-voltage electrode. The results showed an improvement of activity of Bacillus velezensis by the corona discharge treatment was confirmed at an optimum input energy. Mutation of the Bacillus velezensis by the corona discharge treatment was also confirmed through an rRNA sequence alignment analysis. The enzyme activity of the mutated bacteria was greatly improved, which was a positive effect that can meet the production demand.

Case Report: An Eyelid Nodule Caused by Candidatus Dirofilaria hongkongensis Diagnosed by Mitochondrial 12S rRNA Sequence

ABSTRACT. A 59-year-old female living in Rayong Province, eastern Thailand, presented with painless, right upper eyelid nodule for 3 months. Upon removal of the eyelid mass, a well-circumscribed, firm globular mass with diameter about 1 cm was found. Histopathological examination revealed an immature female dirofilarial worm reminiscent of Dirofilaria repens, characterized by prominent sharp longitudinal ridges at external surface of the cuticle. Analysis of the mitochondrial 12S rRNA sequence showed that the worm belongs to Candidatus Dirofilaria hongkongensis. It is likely that some infections previously reported as D. repens based on histological examination may have actually been due to Candidatus D. hongkongensis.

Influence of Pink Pigmented Facultative methylotrophic bacteria (PPFM) as a foliar spraying on the growth and productivity of strawberry(Fragaria xananassa Duch.).

Pink pigmented facultative methylotrophic bacterium (PPFM) has a favorable impact on plant development and production, it is known as a biostimulator, biofertilizer and biocontroller. Here we investigate the effect of foliar spraying of PPFM, 10% methanol,30% methanol, and their combinations on the growth, fruit quality, and yield of two strawberry cultivars. PPFM was isolated from cotton leaves using imprinting technique. 16S rRNA sequence analysis identified it to be Methylobacterium radiotolerance. Its 16S rRNA sequence were deposited in the Gene Bank under accession number MT644122.1. Two field experiments were conducted during the 2017/2018 and 2018/2019 seasons to investigate the effect of foliar spraying of PPFM and methanol (10 and 30%) on the growth, fruit quality, and yield of two strawberry cultivars. The obtained results showed that, there were no significant differences in the most characteristics between the two cultivars except foliage fresh weight and early yield were higher in cv. Florid, however, Festival cv. recorded higher total yield /plant, anthocyanins and ascorbic acid content in both seasons. Spraying PPFM exhibited the highest values of chlorophyll, fresh weight, total yield and quality. Furthermore, PPFM combined with methanol 10% gave the highest values of leaf area, dry matter %, early yield and some fruit quality. Spraying cv. Florida with PPFM resulted in the best interactions for early yield. However, the best interaction for total yield and most fruit quality features was observed with Festival c.v. and spraying PPFM. It is reasonable to conclude that PPFM is the most effective treatment, increasing strawberry total yield/fed by 28.1 % in the 1st season and 27.91 % in the 2 nd season compared to the control.

The Archaeal Transcription Termination Factor aCPSF1 is a Robust Phylogenetic Marker for Archaeal Taxonomy

Archaea represent a unique type of prokaryote, which inhabit in various environments including extreme environments, and so define the boundary of biosphere, and play pivotal ecological roles, particularly in extreme environments. Since their discovery over 40 years ago, environmental archaea have been widely investigated using the 16S rRNA sequence comparison, and the recently developed phylogenomic approach because the majority of archaea are recalcitrant to laboratory cultivation.

Identifying Microbial Interaction Networks Based on Irregularly Spaced Longitudinal 16S rRNA sequence data

Though being vital for human health, microbial interactions with their host and with each other are still largely obscure for researchers. To deepen the understanding, the analyses based on longitudinal data are a better choice than the cross-sectional data since the information provided by the former is usually more stable. To this end, in this paper, we first propose an EM-type algorithm to identify microbial interaction network for the irregularly spaced longitudinal measurements. Correlation functions are employed to account for the correlation across the temporal measurements for a given subject. The algorithms take advantage of the efficiency of the popular graphical lasso algorithm and can be implemented straightforwardly. Simulation studies show that the proposed algorithms can significantly outperform the conventional algorithms such as graphical lasso or neighborhood method when the correlation between measurements grows larger. In second part of the paper, based on a 16S rRNA sequence data set of gut microbiome, module-preserving permutation test is proposed to test the independence of the estimated network and the phylogeny of the microbe species. The results demonstrate evidences of strong association between the interaction network and the phylogenetic tree which indicates that the taxa closer in their genomes tend to have more/stronger interactions in their functions. The proposed algorithms can be implemented through R package lglasso at \url{https://github.com/jiezhou-2/lglasso

Isolation, purification and characterization of mannan degrading enzyme from a new isolate Acinetobacter baummanni

A mannan-degrading microbe was isolated from rotting porang tubers (Amorphophallus muelleri Blume). Molecular identification using 16S-rRNA sequence analysis revealed that the isolate showed 99.67% similarity with Acinetobacter baummanni. A crude enzyme from ammonium sulphate precipitation was used for preliminary characterization. The characterization results showed that the enzyme activity is optimum at 45 °C, and stable at 35-50 °C, while the optimum pH is 7, and stable at pH 5-7. The substrate with the highest relative activity was found in guar gum which was 137.512%. The enzyme activity was inhibited by Ca, Na, K ions, and increased by Mn2+ ions.

Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome

The progression of early childhood caries (ECC) is caused by microbial colonized in dental plaque. However, the association framework both from 16s genus down to high resolution metagenomic strain level and from composition to genome function analysis on caries lacks. 16S rRNA sequence revealed the composition of 3–6 years dental caries (ECC, n = 29), and severe dental caries (SECC, n = 36) children are significantly different from caries-free controls (CF, n = 31). Especially, genus Neisseria is enriched in caries ( P < 0.05 ). Metagenomics sequence of 3 ECCs, 3 SECCs, and 3 CFs reveals Neisseria bacilliformis ATCC BAA-1200 in genus Neisseria is also significantly enriched in caries ( P < 0.05 ). Then, we recovered high-quality metagenomic assembly genomes (MAG), named bin 86, which have 99% identity with Neisseria bacilliformis ATCC BAA-1200 genome. Function analysis of Neisseria bacilliformis ATCC BAA-1200 genome shows its metabolism power of sugar and adhesion, colonization, acid production, and acid tolerance ability, which suggested Neisseria bacilliformis ATCC BAA-1200 may serve as a biomarker for childhood caries.

Characterization of Bacterial Community of Rumen in Dairy Cows With Laminitis

Background: Laminitis- an inflammation of lamella, could cause great economic loss to dairy industry, which has attracted wide attention around the world. In recent years, microbiota is considered as one of the vital parts that played significant role in various diseases processes. However, current studies are far from sufficient. Aim of this study is to explore the characteristics of ruminal microbiota in laminitis cows. Methods: The serum of bovines with or without laminitis was collected to detect concentrations of lipopolysaccharide (LPS), lactic acid, and histamine, and the ruminal fluid was collected for 16S rRNA sequence analysis. Results: The results showed that a significant increase in LPS and lactic acid levels in laminitis group comparing to control group cows. In addition, the higher abundance of bacteria that -riches acid-enhancing metabolites, namely, Candidatus Saccharimonas, Saccharofermentans, Erysipelotrichaceae UCG-009, Erysipelotrichaceae UCG-008, Clostridium papyrosolvens and Ruminococcaceae bacterium AE2021 were detected in the rumen fluid from laminitis bovines. Conclusions: This article confirmed that difference of rumen microbiota were occurred in rumen between health and laminitis bovines. The elevated abundance of bacteria that riches acid- enhancing metabolites, as well as increased the concentration of lactic acid and LPS could be harmful factors to bovines and increase risks of laminitis.

Case Report: An Eyelid Nodule Caused by Candidatus Dirofilaria hongkongensis Diagnosed by Mitochondrial 12S rRNA Sequence

A 59-year-old female living in Rayong Province, eastern Thailand, presented with painless, right upper eyelid nodule for 3 months. Upon removal of the eyelid mass, a well-circumscribed, firm globular mass with diameter about 1 cm was found. Histopathological examination revealed an immature female dirofilarial worm reminiscent of Dirofilaria repens, characterized by prominent sharp longitudinal ridges at external surface of the cuticle. Analysis of the mitochondrial 12S rRNA sequence showed that the worm belongs to Candidatus Dirofilaria hongkongensis. It is likely that some infections previously reported as D. repens based on histological examination may have actually been due to Candidatus D. hongkongensis.

Directed evolution of rRNA improves translation kinetics and recombinant protein yield

In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo.