About
39
Publications
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Introduction
Current institution
Additional affiliations
March 2018 - February 2019
August 2019 - March 2021
April 2021 - August 2021
Education
March 2016 - February 2018
March 2014 - February 2016
March 2010 - February 2014
Korea University
Field of study
- Environmental Science and Ecological Engineering
Publications
Publications (39)
Background
Metabolite production is essential for the proliferation and environmental adaptation of all living organisms. In pathogenic bacteria, metabolite exchange during host infection can regulate their physiology and virulence. However, there is still much unknown about which specific metabolic pathways in pathogenic bacteria respond to change...
Fecal waste from livestock farms contains numerous pathogens, and improperly managed waste may flow into water bodies, causing water-borne diseases. Along with the popularization of high-throughput technologies, community-wide microbial source-tracking methods have been actively developed in recent years. This study aimed to construct a comprehensi...
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiot...
The interspecific responses to alarm signals may be based on unlearned mechanisms but research is often constrained by the difficulties in differentiating between unlearned and learned responses in natural situations. In a field study of two Paridae species, Parus minor and Sittiparus varius, who originated from a common ancestor 8 million years ag...
The gut microbiome of Antarctic fish species has rarely been studied due to difficulties in obtaining samples. The mackerel icefish, Champsocephalus gunnari, primary feeds on krill and is one of the key species in the food web of the Southern Ocean. In this study, we characterized the gut microbiota of C. gunnari by sequencing the V3–V4 region of t...
The river pufferfish (Takifugu obscurus) is a valuable species in aquaculture and genetic studies. Usage of fish anesthetics aids in the easier handling of fish during aquaculture. However, there are no studies on appropriate conditions required for effective anesthetization of pufferfish. This study aims to determine the optimal conditions (fish a...
The interspecific responses to alarm signals may be based on unlearned mechanisms but research is often constrained by the difficulties in differentiating between unlearned and learned responses in natural situations. In a field study of two Paridae species, Parus minor and Sittiparus varius , who originated from a common ancestor 8 million years a...
Chironomidae (chironomid) are one of the dominant families in freshwater ecosystems, and they plays an important role in the food web. They have been used as an indicator for water quality assessment, as they are resistant to diverse environmental pollutants. In this study, we identified the microbiomes of two chironomid species to see if there are...
Archaeal ammonia oxidizers (AOA) are important in converting ammonia into nitrates in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has been poorly understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogen...
Prebiotics are non-digestible food ingredients that promote the growth of beneficial gut microorganisms and foster their activities. The performance of prebiotics has often been tested in mouse models in which the gut ecology differs from that of humans. In this study, we instead performed an in vitro gastrointestinal digestion and fecal fermentati...
Bioaerosols often contain human pathogens and allergens affecting public health. However, relatively little attention has been given to bioaerosols compared with non-biological aerosols. In this study, we aimed to identify bioaerosol compositions in Manchester, UK by applying high throughput sequencing methods and to find potential sources. Samples...
Mineral extraction is known to affect soil fungi in polar environments, but it is unknown how long these effects persist. Here, by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi, we compared soil fungal community in intact natural tundra with that in a nearby former coal mining area, abandoned 52 years previously, on...
Eggshell bacterial communities may affect hatching success and nestling’s condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation...
Edge effects, the altered abiotic and biotic conditions on the borders of natural areas, rarely extend more than a few hundred meters. Edge effects have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if agriculturally-mediated i...
Little is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates acro...
Lead is a toxic environmental contaminant associated with current and historic mine sites. Here we studied the natural attenuation of Pb in a limestone cave system that receives drainage from the ancient Priddy Mineries, UK. Extensive deposits of manganese oxides were observed to be forming on the cave walls and as coatings in the stream beds. Anal...
Primary biological aerosols often include allergenic and pathogenic microorganisms posing potential risks to human health. Moreover, there are airborne plant and animal pathogens that may have ecological and economic impact. In this study, we used high-throughput sequencing techniques (Illumina, MiSeq) targeting the 16S rRNA genes of bacteria and t...
Airborne samples of biological particles were collected using the Uk NERC FAAM research aircraft over Southern England as part of the NERC BIOARC pilot project. Samples were collected within a well developed boundary layer at altitudes from 400 m to 1000 m covering SW England and East Anglia with some profiles over the N. Sea.30 samples were collec...
Anti‐predatory strategies of birds are diverse and may include predator‐specific alarm calls. For example, oriental tit (Parus minor) parents can distinguish snakes from other predators and produce snake‐specific referential vocalizations ("jar" call) when a snake poses a threat to their nest. The “jar” call has a very specific function to induce f...
Despite the extensive, ongoing conversion of tropical forests to rubber plantation, the effects of this land use change on soil fungal community diversity and composition are still poorly known. We compared a network of sites of tropical forest in southern Yunnan, China, with a network of rubber plantation sites originally derived from this forest....
Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAS...
Little is known of how fungal distribution ranges vary with elevation. We studied fungal diversity and community composition from 740 to 2940 m above sea level on Mt. Norikura, Japan, sequencing the ITS2 region. There was a clear trend, repeated across each of the fungal phyla (Basidiomycota, Ascomycota, Zygomycota, Chytridomycota and Glomeromycota...
Nuclear power is an important energy source that can compensate for carbon emissions from fossil fuel power plants. However, processing of radioactive waste from nuclear plants is a significant challenge. The current treatment prior to final geological disposal involves wet storage of spent fuel in designated ponds, and microbial colonisation of th...
Studying how metagenome composition and diversity varies along environmental gradients may improve understanding of the general principles of community and ecosystem structuring. We studied soil bacterial metagenomes along a precipitation gradient on the eastern Tibetan Plateau, varying between 500 mm and 60 mm mean annual precipitation (MAP). We f...
Observations and video documentation of interactions between animals living in dens, cavities, and other enclosed spaces are difficult, but they play an important role in field biology, ecology, and conservation. For example, bird parents visiting nests and feeding their nestlings may provide crucial information for testing of ecological hypotheses...
Predator-specific alarm calls may have a variety of context-specific functions. Parents of the oriental tit, Parus minor, use the 'jar' call in response to the presence of a snake near the nests, and the nestlings respond by escaping the nest cavity. This specific function can be observed only when nestlings are able to fledge. Do tits use the 'jar...
There is considerable interest in the functional basis of ecological strategies amongst bacteria. We used laboratory microcosms based on culturing of elutant from soil, to study the effects of varying initial nutrient concentration, and time succession, on the community metagenome. We found a distinct set of nutrient related or time related changes...
Formation of magnetite in anaerobic sediments is thought to be enhanced by the activities of iron-reducing bacteria. Geobacter has been implicated as playing a major role, as in culture its cells are often associated with extracellular magnetite grains. We studied the bacterial community associated with magnetite grains in sediment of a freshwater...
Questions
Questions (6)
Hi,
Is there a way to get cells growing in the middle of or on the bottom of an agar plate rather than on the surface?
I want to extract DNA from it.
Many studies include rRNA depletion step. However, as far as I know, there is not yet a unified method developed to remove rRNA efficiently.
Do you think improved sequencing depth can compensate for rRNA removal step in studying bacterial metatranscriptome of environmental samples (different species mixed)?
I'm new in RNA works and have a question on preparing cDNA.
I've just read a paper entitled "A simple method for directional transcriptome sequencing using Illumina technology" published in 2009, Nucleic Acids Research, and found that people want to obtain directional information when they study transcriptome.
Is this also an issue studying metatranscriptome (different species mixed)?
Or is it okay to send 1st strand cDNA (single-stranded RNA removed or double-stranded with RNA/cDNA hybrid form) only for sequencing? Or is this dependent on sequencing machine or sequencing company?
I've tried to analyze metagenome data through MG-RAST but cound't find any option to subsample (to normalize) the output annotated sequence abundance. Is there a way to subsample the output file that I got from MG-RAST?
I have extracted bacterial total RNA and got two bands (16S and 23S rRNA and maybe some of invisible mRNA). If I do RT-PCR using random hexamers with this sample and compare the band size I get with the band size of the RNA that I used as a template, cDNA band size should be larger than RNA and there should be multiple bands shown. Is this a right expectation?
