Article
Microbiology
Olakunle Fagbemigun, Gyu-Sung Cho, Niels Roesch, Erik Brinks, Katrin Schrader, Wilhelm Bockelmann, Folarin A. Oguntoyinbo, Charles M. A. P. Franz
Summary: The traditional fermented dairy food Nono from Nigeria was studied for microbial diversity and starter culture development. Analysis identified predominant bacterial species and yeast species involved in milk fermentation, as well as potential pathogens. Selected lactic acid bacteria strains showed potential for improving microbial safety and technological parameters of Nono.
Article
Microbiology
Irina Gladysheva, Yuriy A. Khlopko, Sergey Cherkasov, Vladimir Ya Kataev
Summary: Corynebacterium amycolatum ICIS 99, isolated from vaginal smears of healthy women, exhibits promising antimicrobial activity. The genome analysis reveals that ICIS 99 lacks true virulence factors but possesses genes that contribute to adaptation and survival in the vaginal environment. The genomic information lays the foundation for evaluating the safety and useful properties of ICIS 99 as a potential probiotic strain.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Mie Gammelgaard Jensen, Lejla Svraka, Elena Baez, Michael Lund, Anja Poehlein, Holger Bruggemann
Summary: The pilot study identified a diverse range of Corynebacterium species on human skin, including previously unreported species. The study revealed individual variations in biochemical and resistance profiles among the strains. This highlights the importance of cultivation-based studies in understanding the properties of these microorganisms.
Article
Food Science & Technology
Xiao-min Li, Jie-ying Deng, Wen Nie, Cong Li, Bao-cai Xu
Summary: This study screened and evaluated indigenous starter cultures isolated from dry-cured ducks and found that these strains exhibited excellent safety and probiotic properties, making them suitable as starter cultures to enhance the quality and flavor of dry-cured duck products.
Article
Fisheries
Izzet Burcin Saticioglu, Ertan Emek Onuk, Hilal Ay, Nihed Ajmi, Esra Demirbas, Soner Altun
Summary: In this study, a comprehensive comparison of L. garvieae and L. petauri was conducted through genomic analysis, protein family analysis, and phenotypic analysis. The research revealed the differences and characteristics between the two species. A species-specific primer was designed based on the genome analysis to differentiate L. garvieae and L. petauri, and a sucrose fermentation test was found to be the main phenotypic feature for differentiation. The importance of the research is rated with 8 out of 10.
Article
Microbiology
Nikola Palevich, Faith P. Palevich, Amanda Gardner, Gale Brightwell, John Mills
Summary: The diversity and ecological roles of the genus Shewanella are largely unknown, particularly in relation to their genetic basis and metabolic pathways for food spoilage. In this study, whole-genome sequencing of 32 Shewanella strains isolated from spoiled lamb was conducted to investigate their roles in meat spoilage. Phylogenomic reconstruction revealed genomic diversity within the genus, with some strains belonging to a putative novel species. Pan-genome analysis showed the occurrence of spoilage genes related to sulfur and putrescine metabolism, but the complete set of genes for trimethylamine metabolism was only present in specific strains. Comparative genomics also identified variations in genes associated with adaptation to environmental cues and resistance stresses. This study provides a reference collection of draft Shewanella genomes for future investigations into spoilage mechanisms in the meat industry.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Klaudia Gustaw, Piotr Koper, Magdalena Polak-Berecka, Kamila Rachwal, Katarzyna Skrzypczak, Adam Wasko
Summary: The study describes a newly isolated strain Lactobacillus hilgardii FLUB from mead and characterizes its genome, highlighting its genetic repertoire and unique features. The strain shows a preference for fructose and exhibits resistance to high concentrations of alcohol and sugars, indicating its adaptation to the mead environment. Expertimental research simulating alcoholic beverage conditions confirms the niche specialization of L. hilgardii FLUB.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Aurelie Morand, Mamadou Lamine Tall, Edmond Kuete Yimagou, Issa Isaac Ngom, Cheikh Ibrahima Lo, Florent Cornu, Michel Tsimaratos, Jean-Christophe Lagier, Anthony Levasseur, Didier Raoult, Pierre-Edouard Fournier
Summary: This study describes a new species Anaerococcus urinomassiliensis, isolated from the urine of a 17-year-old boy with autoimmune hepatitis and membranoproliferative glomerulonephritis. The strain exhibits specific genetic characteristics, is primarily of human origin, and belongs to the genus of anaerobic bacteria.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Rita Zgheib, Issam Hasni, Babacar Mbaye, Hussein Anani, Gabriel Haddad, Nicholas Armstrong, Celine Chartier, Aurelia Caputo, Didier Raoult, Florence Fenollar, Pierre-Edouard Fournier
Summary: This article reports the isolation of a strain called Marseille-P9829 from a bone sample collected from a 46-year-old patient with an open right fibula fracture. Through various methods of classification and identification, it was confirmed that this strain belongs to a new species of Buttiauxella, and a proposed name was suggested.
CURRENT MICROBIOLOGY
(2022)
Article
Microbiology
Nichari Bamphensin, Peechanika Chopjitt, Rujirat Hatrongjit, Parichart Boueroy, Nahuel Fittipaldi, Marcelo Gottschalk, Anusak Kerdsin
Summary: S. suis isolates from human infections in Thailand showed susceptibility to cefepime and ceftriaxone, but high resistance to tetracycline, clindamycin, erythromycin, and azithromycin. Macrolide- and tetracycline-resistant isolates had predominant resistance genes tet(O) and ermB. Penicillin-intermediate resistance isolates mainly belonged to serotype 2-ST233. Analysis of PBP protein sequences revealed multiple amino acid substitutions in non-penicillin-susceptible isolates.
Article
Food Science & Technology
Ahmet E. Yetiman, Abdullah Keskin, Busra Nur Darendeli, Seyfullah Enes Kotil, Fatih Ortakci, Mahmut Dogan
Summary: In this study, a new strain of Lactiplantibacillus plantarum, DY46, was isolated from a traditional fermented beverage and its genome was sequenced and analyzed. The DY46 genome contains a variety of genes encoding enzymes and antimicrobial factors, indicating its potential as a probiotic. It also shows tolerance to gastrointestinal conditions.
Article
Veterinary Sciences
Lin Li, Zhenzhong Wang, Chuanxiang Qi, Shan Liu, Mingxia Gong, Jinming Li, Xiaodong Wu, Zhiliang Wang
Summary: Lumpy skin disease (LSD) is an infectious disease caused by lumpy skin disease virus (LSDV). This study detected and analyzed LSDV isolates from the Yili area and Fujian province in China. The isolates were identified as LSDV and showed high similarity to strains from East and Southeast Asia. Recombination events were also observed in the isolates.
BMC VETERINARY RESEARCH
(2022)
Article
Plant Sciences
Juliana Gonzalez-Tobon, Tyler C. Helmann, Margery Daughtrey, Paul V. Stodghill, Melanie J. Filiatrault
Summary: In this study, the complete and annotated genome sequence of Xanthomonas hortorum strain 108, isolated from Greek oregano in Long Island, NY, U.S.A., was reported.
Article
Multidisciplinary Sciences
Diganta Narzary, Nitesh Boro, Ashis Borah, Takashi Okubo, Hideto Takami
Summary: The study reveals the complex microbial community structure and metabolic functions of emao using shotgun whole-metagenome sequencing technology; eukaryotic microorganisms dominate over prokaryotes in emao, holding a significant position in microbial abundance.
SCIENTIFIC REPORTS
(2021)
Article
Agricultural Engineering
Qi Sheng, Xiaoyu Wu, Yan Jiang, Zhimin Li, Fei Wang, Bin Zhang
Summary: This study demonstrated the biobased production of L-ornithine from mannitol using engineered Corynebacterium glutamicum, providing a reference for the production of additional chemicals from mannitol.
BIORESOURCE TECHNOLOGY
(2021)
Article
Microbiology
Changsu Lee, Hye Seon Song, Se Hee Lee, Joon Yong Kim, Jin-Kyu Rhee, Seong Woon Roh
Summary: In this study, three facultatively oligotrophic haloarchaea were isolated from solar salt and their complete genomes were sequenced, revealing the presence of carbohydrate-active enzyme genes and stress-tolerance protein genes that may have industrial applications. The genome data generated will facilitate further research on halophilic strains and their potential industrial uses.
ARCHIVES OF MICROBIOLOGY
(2021)
Review
Microbiology
Tae Woong Whon, Na-Ri Shin, Joon Yong Kim, Seong Woon Roh
Summary: Recent advances in environmental microbial genomics have improved our understanding of the interactions between microbial communities and their niche in the host gut; integration of various omics data to study the gut microbiome has become increasingly common, although downstream analysis and interpretation of complex omics data remain challenging. Studies have explored gut microbiome characteristics using omics approaches, and recent discussions have focused on analytics programs and advanced techniques for further utilization of omics data.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Microbiology
Tae Woong Whon, Hyun Sik Kim, Na-Ri Shin, Hojun Sung, Min-Soo Kim, Joon Yong Kim, Woorim Kang, Pil Soo Kim, Dong-Wook Hyun, Hoon Je Seong, Woo Jun Sul, Seong Woon Roh, Jin-Woo Bae
Summary: Neonatal calf diarrhea is a major cause of economic loss for cattle producers worldwide, with multifactorial etiology making disease control challenging. The study reveals microbial compositional and functional dysbiosis in the gut of diarrheic calves, potentially contributing to the onset of diarrhea. Additionally, it suggests that prolonged expansion of nontoxigenic Enterobacteriaceae in the gut may play a role in the development of calf diarrhea.
Article
Microbiology
Juseok Kim, Joon Yong Kim, Hye Seon Song, Yeon Bee Kim, Tae Woong Whon, Seung Woo Ahn, Se Hee Lee, SeungRan Yoo, Yu Jin Kim, Jinjong Myoung, Yoon-E Choi, Hong-Seok Son, Seong Woon Roh
Summary: The novel species Anaerocolumna sedimenticola sp. nov. (CBA3638(T)) was isolated from the Geum River sediment in South Korea and belongs to the genus Anaerocolumna. The strain exhibits Gram-stain-positive, anaerobic characteristics with specific cell size and morphology. Detailed information on the genome characteristics and growth conditions of this strain are also provided.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2021)
Article
Food Science & Technology
Hye Seon Song, Se Hee Lee, Seung Woo Ahn, Joon Yong Kim, Jin-Kyu Rhee, Seong Woon Roh
Summary: The main ingredients of kimchi play a crucial role in determining the microbial community and metabolite composition during food fermentation. Microorganisms such as Leuconostoc gelidum, Weissella kandleri, and Lactobacillus sakei groups were found to be primarily distributed in kimchi cabbage and young radish-based foods. The metabolite profiles varied depending on the sample type, suggesting that the main ingredients significantly impact the fermentation process.
FOOD RESEARCH INTERNATIONAL
(2021)
Correction
Food Science & Technology
Hye Seon Song, Se Hee Lee, Seung Woo Ahn, Joon Yong Kim, Jin-Kyu Rhee, Seong Woon Roh
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Food Science & Technology
Joon Yong Kim, Seong-Eun Park, Eun-Ju Kim, Seung-Ho Seo, Tae Woong Whon, Kwang-Moon Cho, Sun Jae Kwon, Seong Woon Roh, Hong-Seok Son
Summary: This study investigated the succession of microorganisms and changes in metabolites during long-term fermentation of kimchi. The dominant taxa shifted from Leuconostoc and Weissella in the early stages to Latilactobacillus and Levilactobacillus in the middle and late stages. The metabolite analysis showed that about half of the metabolites were produced within the first 15 days of fermentation. These findings highlight the dynamic nature of microbiota and the evolving composition of metabolites during long-term fermentation.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Food Science & Technology
Namhee Kim, Jieun Lee, Hye Seon Song, Young Joon Oh, Min-Sung Kwon, Misun Yun, Seul Ki Lim, Hyo Kyeong Park, Young Seo Jang, Sulhee Lee, Sang-Pil Choi, Seong Woon Roh, Hak-Jong Choi
Summary: This study found that kimchi can suppress obesity-induced inflammation and exert its effects by changing gut microbiota composition and short-chain fatty acids production.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Food Science & Technology
Mi-Ja Jung, Juseok Kim, Se Hee Lee, Tae Woong Whon, Hojun Sung, Jin-Woo Bae, Yoon-E Choi, Seong Woon Roh
Summary: This study reveals the ecological role of LAB starters in the fermentation of kimchi and investigates the potential impact of bacteriophages on the fermentation properties of kimchi.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Chang Hee Jeong, Joon Yong Kim, Young Joon Oh, Hye In Ko, Seong Woon Roh, Sung Wook Hong, Hyuk Cheol Kwon, Sung Gu Han, Tae Woon Kim
Summary: This study assessed the safety of white colony-forming yeasts (WCFYs), finding that they did not induce toxic responses in cell and animal experiments, and genomic analysis showed that one of the yeasts did not harbor genes related to toxicity and antimicrobial resistance.
Article
Microbiology
Juseok Kim, Seong Woo Ahn, Joon Yong Kim, Tae Woong Whon, Seul Ki Lim, Byung Hee Ryu, Nam Soo Han, Hak-Jong Choi, Seong Woon Roh, Se Hee Lee
Summary: This study found that the ingestion of lactic acid bacteria can alleviate the ill effects of alcoholic liver disease, including inflammation, liver damage, gut dysbiosis, and abnormal intestinal nutrient metabolism.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Hae-In Joe, Jee-Won Choi, June-Young Lee, Hojun Sung, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, Jin-Woo Bae
Summary: Three new bacterial strains, 321(T), 335(T), and 353(T), were isolated from the intestines of Aegosoma sinicum larvae collected in Paju-Si, South Korea. These strains belong to the genus Luteibacter and are characterized as Gram-negative, obligate aerobes with rod-shaped cells and a single flagellum. Through genomic analysis, it is determined that these strains are novel species within the genus Luteibacter.
JOURNAL OF MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Min-Soo Kim, Eun-Jin Park
Summary: This study investigated the fungal communities on the surfaces of broccoli florets collected from 22 farms across four regions in Korea. It identified core genera specific to the broccoli phyllosphere and found that the composition and complexity of these communities varied among farming regions and were associated with agro-meteorological conditions.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Microbiology
Hye Seon Song, Juseok Kim, Yeon Bee Kim, Se Hee Lee, Tae Woong Whon, Seong Woon Roh
Summary: Two novel halophilic archaeal strains were isolated from solar salt in South Korea. Through genetic, physiological, and biochemical analyses, they were found to represent a new genus and species in the family Halobacteriaceae.
JOURNAL OF MICROBIOLOGY
(2022)
Article
Microbiology
Yujin Kim, Yeon Bee Kim, Juseok Kim, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Eun-Ji Song, Young-Do Nam, Se Hee Lee, Seong Woon Roh
Summary: Two novel bacterial strains, CBA3104(T) and CBA3105(T), isolated from kimchi, were identified as a new species of Brachybacterium genus (Brachybacterium kimchii sp. nov.) and a new subspecies of B. halotolerans (B. halotolerans subsp. kimchii subsp. nov.), respectively. These strains showed differences in growth conditions and genetic similarity.
JOURNAL OF MICROBIOLOGY
(2022)
