Ethanol-related transcriptomic changes in mouse testes.

Background: Alcohol consumption is widely known to have detrimental effects on various organs and tissues. The effects of ethanol on male reproduction have been studied at the physiological and cellular levels, but no systematic study has examined the effects of ethanol on male reproduction-related gene expression.

Results: We employed a model of chronic ethanol administration using the Lieber-DeCarli diet.

Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp () aquaculture system.

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented.

A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments.

Tidal-flat sediments harbor a diverse array of sulfate-reducing bacteria. To isolate novel sulfate-reducing bacteria and determine their abundance, a tidal-flat sediment sample collected off Ganghwa Island (Korea) was investigated using cultivation-based and culture-independent approaches. Two Gram-stain-negative, strictly anaerobic, rod-shaped, sulfate-reducing bacteria, designated IMCC35004 and IMCC35005, were isolated from the sample.

Uliginosibacterium aquaticum sp. nov., Isolated from a Freshwater Lake.

A Gram-stain-negative, aerobic, chemoheterotrophic, rod-shaped bacterium motile by a polar flagellum, designated IMCC34675, was isolated from Chungju Lake, an artificial freshwater reservoir in Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC34675 belongs to the genus Uliginosibacterium, sharing ≤ 97.1% sequence similarities with the type strains of the genus.

sp. nov., isolated from a freshwater stream.

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated as IMCC34836, was isolated from a freshwater stream. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34836 was most closely related to HW001 (of the family ) with 95.6 % sequence similarity and formed a robust clade with HW001.

High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.

Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives.

sp. nov., isolated from a freshwater lake.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678 belongs to the genus with ≤98.7 % sequence similarities to species.

sp. nov., isolated from freshwater.

A Gram-stain-negative, rod-shaped, obligately aerobic, motile by a single polar flagellum, chemoheterotrophic bacterium, designated strain IMCC25680, was isolated from surface water in Chungju Lake, Republic of Korea. 16S rRNA gene sequence analysis revealed that strain IMCC25680 was most closely related to HW7 with 95.5% sequence similarity and formed a robust clade with HW7.

sp. nov. and sp. nov., Fe(III)-reducing bacteria isolated from marine environments.

Two Gram-stain-negative, Fe(III)-reducing, facultatively anaerobic, motile via a single polar flagellum, rod-shaped bacterial strains, designated IMCC35001 and IMCC35002, were isolated from tidal flat sediment and seawater, respectively. Results of 16S rRNA gene sequence analysis showed that IMCC35001 and IMCC35002 shared 96.6 % sequence similarity and were most closely related to FUT3661 (98.

Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater.

A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1B (94.5%) and Halioglobus pacificus S1-72 (94.

sp. nov. and sp. nov., isolated from freshwater environments.

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753 and IMCC26285, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to JC216(98.

sp. nov., isolated from coastal seawater.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385 represented a member of the genus sharing 94.6-97.

Photochemical characterization of flavobacterial rhodopsin: The importance of the helix E region for heat stability.

Although many microbial rhodopsins have been discovered many of organisms in a variety of habitats, little is known about the property and diversity of rhodopsin in flavobacteria. Recent studies discovered that many proteorhodopsin (PR)-like proteins exist in genomes of flavobacteria. Following the isolation of a flavobacterial rhodopsins (FR) from the flavobacteria IMCC1997 from the East Sea of Korea, we characterized its photochemical features.

Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta.

Microalgae and bacteria are known to be closely associated in diverse environments. To isolate dominant bacterial species associated with a green alga, Dunaliella tertiolecta, a photoreactor culture of the microalga was investigated using culture-based and culture-independent approaches. The bacterial community structure of the algal culture showed that the most abundant bacterial species under the culture conditions was related to the genus Winogradskyella.

sp. nov., isolated from a large freshwater lake.

A Gram-staining-negative, aerobic, motile with a single polar flagellum and rod-shaped bacterium as a bacterial host of podovirus P26218, designated IMCC26218, was isolated from Lake Soyang, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC26218 belonged to the genus of the family and shared 97.7-99.

Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322.

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture.

sp. nov., isolated from tidal flat sediment.

A Gram-stain-negative, obligately aerobic, cream-coloured, non-gliding, motile with a single polar flagellum and rod-shaped bacterium, designated IMCC34151, was isolated from tidal flat sediment of the Yellow Sea, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34151 belonged to the genus of the family and shared 94.7-96.

Sulfitobacter profundi sp. nov., isolated from deep seawater.

A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263 belonged to the genus Sulfitobacter and shared 96.1-99.

Genome analysis of Rubritalea profundi SAORIC-165, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean.

Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R.

Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River.

A non-motile, yellow-pigmented bacterial strain, designated IMCC34762, was isolated from a freshwater sample collected from Lake Cheongpyeong in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC-34762 formed a lineage within the genus Flavobacterium and was most closely related to F. pectinovorum DSM 6368 (98.

Nibricoccus aquaticus gen. nov., sp. nov., a new genus of the family Opitutaceae isolated from hyporheic freshwater.

A yellow-coloured, Gram-strain-negative, non-motile, cocci-shaped, strictly aerobic bacterium, designated HZ-65, was isolated from hyporheic freshwater in the Republic of Korea. Strain HZ-65 grew at 15-37 °C (optimum, 25-30 °C), pH 5.5-9.

Flavobacterium hydrophilum sp. nov. and Flavobacterium cheongpyeongense sp. nov., isolated from freshwater.

Two Gram-stain-negative, non-motile, yellow-pigmented bacterial strains, designated IMCC34758 and IMCC34759, were isolated from freshwater. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains formed a distinct clade within the genus Flavobacterium and they shared 97.9 % sequence similarity.

Winogradskyella aurantiaca sp. nov., isolated from seawater.

A Gram-stain-negative, non-flagellated, motile-by-gliding, orange-coloured bacterial strain, designated strain IMCC20180, was isolated from seawater collected off the coast of the East Sea in the Republic of Korea. The 16S rRNA gene sequence analysis showed that strain IMCC20180 was most closely related to Winogradskyellaporiferorum UST030701-295 (95.7 % sequence similarity) and formed a robust phylogenetic clade with other Winogradskyella species, indicating that the strain was affiliated with the genus Winogradskyella.

Pedobacter aquicola sp. nov., isolated from freshwater.

A non-motile, pink-pigmented bacterial strain designated IMCC25679, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679 formed a lineage within the genus Pedobacter. The strain IMCC25679 was closely related to Pedobacter daechungensis Dae 13 (96.