16S rRNA amplicon sequencing of intestinal microbiota in Eurasian Wigeon around Osaka, Japan.

We report 16S rRNA gene amplicon data on the succession of intestinal microbiomes in migratory bird, Eurasian Wigeon (Mareca Penelope) wintering around Osaka, Japan. This study could serve as baseline data for comparison with microbiomes in migratory birds.

Impact of Different Attitudes toward Face-to-Face and Online Classes on Learning Outcomes in Japan.

During the coronavirus disease 2019 (COVID-19) pandemic, online-based learning has become mainstream in many countries, and its learning outcomes have been evaluated. However, various studies have shown that online-based learning needs to be optimized in the future, and the number of reports for this purpose is currently not sufficient. The purpose in this study was to determine the relationship between academic performance and attitudes toward face-to-face and remote formats among Japanese pharmacy students enrolled in a course designed for knowledge acquisition.

Genome Sequence of Colistin-Resistant Escherichia coli CLR8, Isolated from the Feces of Larus argentatus.

Migratory birds are potential vehicles of antibiotic-resistant bacteria. In this study, a colistin-resistant strain, CLR8, was isolated from the feces of The draft genome sequence of the strain indicated that it hosts , which is a plasmid-mediated colistin resistance gene.

Positive Selection in F-Box Domain (lpp0233) Encoded in Legionella pneumophila Strains.

　Recent studies have shown that the genome of Legionella pneumophila is characterized by many foreign genes from a variety of eukaryotes. The eukaryotic like proteins are known to play a role in its multiplication within host cells; however, their evolutionary genetics of L. pneumophila in environments is unknown.

Draft Genome Sequence of Multidrug-Resistant Stenotrophomonas pavanii BWK1, Isolated from Mareca penelope Feces.

Migratory birds serve as vectors by transmitting antibiotic-resistant bacteria across large distances. Here, we isolated a multidrug-resistant strain, BWK1, from feces. Analysis of the draft genome sequence of the isolated strain indicated that BWK1 harbors a class A beta-lactamase, metallo-beta-lactamase, and several multidrug efflux pumps.

Draft Genome Sequence of Carbapenem-Resistant Pseudomonas fluorescens Strain BWKM6, Isolated from Feces of Mareca penelope.

Migratory birds are potential vehicles of antibiotic-resistant bacteria. Here, we isolated the multidrug-resistant strain BWKM6 from the feces of The strain's draft genome sequence indicates that it harbors a metallo-beta-lactamase, a class C beta-lactamase, and several multidrug efflux pumps.

[Intestinal Microbiota in Migrating Barn Swallows around Osaka].

 Migratory birds are considered as vectors of infectious diseases, owing to their potential for transmitting pathogens over large distances. The populations of barn swallow (Hirundo rustica) migrate from Southeast Asia to the Japanese mainland during spring and migrate back to Southeast Asia during autumn. This migratory population is estimated to comprise approximately hundreds to thousands of individuals per year.

Draft Genome Sequence of Extended-Spectrum Beta-Lactamase-Producing BWK15 Isolated from Feces of .

Migratory birds have been postulated as potential vehicles of antibiotic resistance. Here we isolated the extended-spectrum beta-lactamase (ESBL)-producing strain BWK15 from the feces of The strain's draft genome sequence indicated that it harbors class A ESBL, class C beta-lactamase, and many multidrug efflux pumps.

Draft Genome Sequence of Multidrug-Resistant sp. Strain KWT-B, Isolated from Feces of .

Migratory birds have been postulated as potential spreaders of antibiotic resistance. Multidrug-resistant sp. strain KWT-B was isolated from the feces of A draft genome sequence indicated that the strain harbors multidrug-resistant transporters, multidrug efflux pumps, a vancomycin-resistant protein, and metallo-beta-lactamases.

Draft Genome Sequences of Amoeba-Resistant Aeromonas spp. Isolated from Aquatic Environments.

Amoeba-resistant Aeromonas veronii ARB3 and Aeromonas media ARB13 and ARB20, which may be important intracellular pathogens of eukaryotic hosts, were isolated from pond and river waters. The draft genome sequences indicate that the strains harbor multiple protein secretion systems and toxins that induce disruption of the actin cytoskeleton.

Draft Genome Sequence of an Antifungal Bacterium Isolated from the Breeding Environment of Dorcus hopei binodulosus.

Burkholderia sp. strain A1 was isolated from a decaying log present in the breeding environment of a stag beetle. The draft genome sequence indicates that strain A1 harbors many biosynthesis molecules, which have antimicrobial properties, and thus potentially eliminates the fungi by producing antifungal compounds, such as siderophores.

Break down of asian dust particle on wet surface and their possibilities of cause of respiratory health effects.

Asian dust (called 'Kosa' in Japan) is comprised of a large number of soil particles originating from the arid regions and deserts of China and Mongolia and dispersed long-range to Japan. A major public concern about Asian dust is its impact on human health. We collected Asian dust particles over the Japan Sea at an altitude of 900 m to directly estimate their effects on health.

High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level.

Lateral gene transfer by phages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency and range of phage-mediated gene transfer, it is important to understand the movement of DNA among microbes. Using an in situ DNA amplification technique (cycling primed in situ amplification-fluorescent in situ hybridization; CPRINS-FISH), we examined the propensity for phage-mediated gene transfer in freshwater environments at the single-cell level.

Soil microbial community structure in an Asian dust source region (Loess plateau).

The bacterial community structure in four geographically isolated arid regions on the Loess plateau, China, a source of Asian dust, was investigated using a 16S rRNA gene. Denaturing gradient gel electrophoresis and sequencing demonstrated that community diversity in the Loess plateau was low, and a common Alphaproteobacteria phylotype was identified. Phylogenetic analyses of arid soils revealed that most phylotypes had low similarity with known strains in various phyla, suggesting that these regions contain phylogenetically divergent and unknown bacteria.

Similarity of bacterial community structure between Asian dust and its sources determined by rRNA gene-targeted approaches.

The atmospheric movement of arid soil can play an important role in the movement of microorganisms attached to soil microparticles. Bacterial community structures in Asian dust collected at Beijing were investigated using the 16S rRNA gene sequence and compared to those in arid soil, a possible source of the dust. Asian dust samples contained 2.

Transfer of a phage T4 gene into Enterobacteriaceae, determined at the single-cell level.

The transfer range of phage genes was investigated at the single-cell level by using an in situ DNA amplification technique. After absorption of phages, a phage T4 gene was maintained in the genomes of non-plaque-forming bacteria at frequencies of 10(-2) gene copies per cell. The gene transfer decreased the mutation frequencies in nonhost recipients.

Application of real-time long and short polymerase chain reaction for sensitive monitoring of the fate of extracellular plasmid DNA introduced into river waters.

The precise estimation of extracellular DNA, long enough to encode a gene, is valuable for determining its potential involvement in genetic transformation. Here, the applicability of real-time long PCR was examined by using target DNA of different lengths and transformation with competent cells to monitor the fate of plasmid DNA released into rivers. Detection limits of the PCR were 7 and 30 copies reaction(-1) for a plasmid (4.

High-frequency phage-mediated gene transfer among Escherichia coli cells, determined at the single-cell level.

Recent whole-genome analysis suggests that lateral gene transfer by bacteriophages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency of phage-mediated gene transfer, we employed cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) and investigated the movement of the ampicillin resistance gene among Escherichia coli cells mediated by phage at the single-cell level. Phages P1 and T4 and the newly isolated E.

Quantitative determination of free-DNA uptake in river bacteria at the single-cell level by in situ rolling-circle amplification.

Detection of plasmid DNA uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (RCA). Uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in Osaka, Japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. Plasmid uptake determined by in situ RCA was compared to direct counts of cells expressing gfp under fluorescence microscopy to examine differences in detection sensitivities between the two methods.

Genetic and physiological characterization of the intestinal bacterial microbiota of Bluegill (Lepomis macrochirus) with three different feeding habits.

Bluegill (Lepomis macrochirus) in Lake Biwa, Japan, feed on benthic invertebrates (benthivorous type), aquatic plants (herbivorous type), and zooplankton (planktivorous type). To evaluate the effect of food on intestinal bacterial microbiota, we characterized and compared the intestinal microbiota of these three types of bluegill in terms of community-level physiological profile (CLPP) and genetic structure. The CLPP was analyzed using Biolog MicroPlates (Biolog, Inc.

Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification.

Rolling circle amplification (RCA) generates large single-stranded and tandem repeats of target DNA as amplicons. This technique was applied to in situ nucleic acid amplification (in situ RCA) to visualize and count single Escherichia coli cells carrying a specific gene sequence. The method features (i) one short target sequence (35 to 39 bp) that allows specific detection; (ii) maintaining constant fluorescent intensity of positive cells permeabilized extensively after amplicon detection by fluorescence in situ hybridization, which facilitates the detection of target bacteria in various physiological states; and (iii) reliable enumeration of target bacteria by concentration on a gelatin-coated membrane filter.

Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification.

Cycling primed in situ amplification-fluorescent in situ hybridization (CPRINS-FISH) was developed to recognize individual genes in a single bacterial cell. In CPRINS, the amplicon was long single-stranded DNA and thus retained within the permeabilized microbial cells. FISH with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria.

rRNA sequence-based scanning electron microscopic detection of bacteria.

A new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rRNA-targeted oligonucleotide probes (SEM-ISH). Target cells were hybridized with oligonucleotide probes after gold labeling. Gold enhancement was used for amplification of probe signals from hybridized cells.

Simplified sample preparation using frame spotting method for direct counting of total bacteria by fluorescence microscopy.

A new preparation method for direct counting of bacteria in liquid samples with fluorescence microscope was developed using a glass slide coated with 3-aminopropyltriethoxy silane and ring-shaped polyester seal as a retainer. The experimental steps of this method were spotting samples onto the coated slides with the seal, drying under vacuum, staining with SYBR Green II, drying and covering with immersion oil and coverslip to allow counting. This simplified method provided consistent results when compared with the conventional filtration method for fluorescence microscopy, and is rapid, inexpensive and reproducible.