• Korean Journal of Microbiology
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• v.53 no.1
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• pp.29-38
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• 2017

In this study, we investigated the phylogenetic diversity of the bacterial community and isolation of extremely halophilic bacteria using culturomics in a gray solar saltern. The number of bacterial living cells, enumerated in a gray solar saltern by direct fluorescence microscopy was three to four orders of magnitude greater than those enumerated by plate counts, suggesting the distribution of 'viable but non-culturable bacteria'. The biodiversity of bacterial communities in a gray solar saltern was investigated by pyrosequencing, 1,778 OTUs of bacteria were comprised of 18 phyla 46 classes 85 orders 140 families 243 genera with 6.16 diversity index. Archaea communities were composed of 3 phyla 6 classes 7 orders 7 families 38 genera with 4.95 diversity index from 643 OTUs. Totally 137 isolates were isolated by 59 different cultural methods based on culturomics considering culture media and conditions suitable for the growth of extremely halophilic bacteria. Phylogenetic analyses of extremely halophilic isolates based on 16S rRNA gene sequences, extremely halophilic isolates were composed of 4 phyla and 11 genera. Haloterrigena and Haloferax can be successfully isolated from culturomics. These culturomics were effective methods for collection of diversity of extremely halophilic bacteria.

• Journal of Microbiology and Biotechnology
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• v.34 no.4
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• pp.757-764
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• 2024

Despite considerable advancements achieved using next-generation sequencing technologies in exploring microbial diversity, several species of the gut microbiome remain unknown. In this transformative era, culturomics has risen to prominence as a pivotal approach in unveiling realms of microbial diversity that were previously deemed inaccessible. Utilizing innovative strategies to optimize growth and culture medium composition, scientists have successfully cultured hard-tocultivate microbes. This progress has fostered the discovery and understanding of elusive microbial entities, highlighting their essential role in human health and disease paradigms. In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1423-1432
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• 2021

To elucidate the role and mechanism of microbes, we combined culture-dependent and culture-independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.

• Mass Spectrometry Letters
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• v.13 no.4
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• pp.106-114
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• 2022

A rapid and reliable approach to the identification of microorganisms is a critical requirement for large-scale culturomics analysis. MALDI-TOF MS is a suitable technique that can be a better alternative to conventional biochemical and gene sequencing methods as it is economical both in terms of cost and labor. In this review, the applications of MALDI-TOF MS for the comprehensive identification of microorganisms and bacterial strain typing for culturomics-based approaches for various environmental studies including bioremediation, plant sciences, agriculture and food microbiology have been widely explored. However, the restriction of this technique is attributed to insufficient coverage of the mass spectral database. To improve the applications of this technique for the identification of novel isolates, the spectral database should be updated with the peptide mass fingerprint (PMF) of type strains with not only microbes with clinical relevance but also from various environmental sources. Further, the development of enhanced sample processing methods and new algorithms for automation and de-replication of isolates will increase its application in microbial ecology studies.

• Journal of Wetlands Research
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• v.23 no.4
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• pp.364-371
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• 2021

Public awareness of alien species can vary by generation, period, or specific events associated with these species. An understanding of public awareness is important for the management of alien species because differences in public awareness can affect the establishment and implementation of management plans. We analyzed digital texts on social media platforms, news articles, and internet search volumes used in conservation culturomics to understand public interest and sentiment regarding alien freshwater species. The number of tweets, number of news articles, and relative search volume to 11 freshwater alien species were extracted to determine public interest. Additionally, the trend over time, seasonal variability, and repetition period of these data were confirmed. We also calculated the sentiment score and analyzed public sentiment in the collected data using sentiment analysis based on text mining techniques. The American bullfrog, nutria, bluegill, and largemouth bass drew relatively more public interest than other species. Some species showed repeated patterns in the number of Twitter posts, media coverage, and internet searches found according to the specified periods. The text mining analysis results showed negative sentiments from most people regarding alien freshwater species. Particularly, negative sentiments increased over the years after alien species were designated as ecologically disturbing species.

• Annual Conference on Human and Language Technology
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• 2017.10a
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• pp.175-178
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• 2017

본 연구는 거시적 빅데이터 인문학과 미시적 언어 텍스트 검색 시스템을 구축하고, 이를 통해서 언어를 통한 문화의 역동적 변화를 시간적 순서에 따라 살펴보고자 한다. 연구의 최종적인 목표는 문화도 생물체처럼 변화하는 존재라 여기고 그 구성요소들을 연구한다는 뜻인 '문화체학(文化體學; Culturomics)'과 같은 '인문학 + 정보과학 + 사회과학' 등등의 다학문간의 융합적 연구에 있다. 이 시스템을 통해서 인류 역사의 기록인 텍스트 빅데이터를 통한 인문학적 성찰을 시각화하고 있다. 이러한 구글의 업적은 인문학과 정보기술의 융합을 통해서 인문학 자체의 지평을 넓히고, 사회과학을 변형시키고, 산업과 상아탑 사이의 관계를 재조정하는데 있다.

• 한국어정보학회:학술대회논문집
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• 2017.10a
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• pp.175-178
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• 2017

본 연구는 거시적 빅데이터 인문학과 미시적 언어 텍스트 검색 시스템을 구축하고, 이를 통해서 언어를 통한 문화의 역동적 변화를 시간적 순서에 따라 살펴보고자 한다. 연구의 최종적인 목표는 문화도 생물체처럼 변화하는 존재라 여기고 그 구성요소들을 연구한다는 뜻인 '문화체학(文化體學; Culturomics)'과 같은 '인문학 + 정보과학 + 사회과학' 등등의 다학문간의 융합적 연구에 있다. 이 시스템을 통해서 인류 역사의 기록인 텍스트 빅데이터를 통한 인문학적 성찰을 시각화하고 있다. 이러한 구글의 업적은 인문학과 정보기술의 융합을 통해서 인문학 자체의 지평을 넓히고, 사회과학을 변형시키고, 산업과 상아탑 사이의 관계를 재조정하는데 있다[1].

• Food Science of Animal Resources
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• v.44 no.5
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• pp.1080-1095
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• 2024

In contemporary society, the increasing number of pet-owning households has significantly heightened interest in companion animal health, expanding the probiotics market aimed at enhancing pet well-being. Consequently, research into the gut microbiota of companion animals has gained momentum, however, ethical and societal challenges associated with experiments on intelligent and pain-sensitive animals necessitate alternative research methodologies to reduce reliance on live animal testing. To address this need, the Fermenter for Intestinal Microbiota Model (FIMM) is being investigated as an in vitro tool designed to replicate gastrointestinal conditions of living animals, offering a means to study gut microbiota while minimizing animal experimentation. The FIMM system explored interactions between intestinal microbiota and probiotics within a simulated gut environment. Two strains of commercial probiotic bacteria, Enterococcus faecium IDCC 2102 and Bifidobacterium lactis IDCC 4301, along with a newly isolated strain from domestic dogs, Lactobacillus acidophilus SLAM AK001, were introduced into the FIMM system with gut microbiota from a beagle model. Findings highlight the system's capacity to mirror and modulate the gut environment, evidenced by an increase in beneficial bacteria like Lactobacillus and Faecalibacterium and a decrease in the pathogen Clostridium. The study also verified the system's ability to facilitate accurate interactions between probiotics and commensal bacteria, demonstrated by the production of short-chain fatty acids and bacterial metabolites, including amino acids and gamma-aminobutyric acid precursors. Thus, the results advocate for FIMM as an in vitro system that authentically simulates the intestinal environment, presenting a viable alternative for examining gut microbiota and metabolites in companion animals.