Article
Microbiology
Senying Lai, Yan Yan, Yanni Pu, Shuchun Lin, Jian-Ge Qiu, Bing-Hua Jiang, Marisa Isabell Keller, Mingyu Wang, Peer Bork, Wei-Hua Chen, Yan Zheng, Xing-Ming Zhao
Summary: In this study, researchers analyzed 3363 fungal sequencing samples from 16 cohorts and identified four mycobiome enterotypes. These enterotypes were stable across different populations and geographical locations and showed significant correlation with bacterial enterotypes. Notably, the fungal enterotypes were strongly associated with age, with the Candida-dominated enterotype being enriched in the elderly population and increasing the risk of multiple diseases related to compromised intestinal barrier. The study also found a fungi-contributed aerobic respiration pathway that mediated the association between compromised intestinal barrier and aging. Overall, the human gut mycobiome has stable compositional patterns and is significantly correlated with various host factors such as diseases and age.
Article
Biochemistry & Molecular Biology
Tianyu Fu, Lin Pan, Qingsen Shang, Guangli Yu
Summary: Different microbiota compositions have varying effects on the fermentation of alginate and its derivatives, with Bacteroides-dominated microbiota showing greater proficiency in degrading and utilizing these polysaccharides. Microbiota composition dictates the amount of short-chain fatty acids produced, with Bacteroides-dominated microbiota yielding the highest total SCFAs and butyrate in the fermentation of alginate and polymannuronate acid.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Ran Li, Yongming Wang, Han Hu, Yan Tan, Yingfei Ma
Summary: By conducting a comprehensive analysis of the archaeal viruses in the human gut metagenomes and existing virus collections, we have revealed the unexplored diversity of archaeal viruses and uncovered a novel facet of the human gut microbiome.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-Francois Brugere, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger
Summary: The study analyzed 1,167 nonredundant archaeal genomes from human gut microbiomes, revealing previously undescribed genera, associations with sociodemographic factors, and the presence of an archaeal virome. The research demonstrates that archaea exhibit specific genomic and functional adaptations to the host, carrying a complex virome that plays a role in human physiology. This work expands our understanding of the human archaeome and provides a genome catalogue for future studies.
NATURE MICROBIOLOGY
(2022)
Article
Microbiology
Mi Young Lim, Seungpyo Hong, So-Jung Bang, Won-Hyong Chung, Ji-Hee Shin, Jung-Ha Kim, Young-Do Nam
Summary: This study characterized the gut microbiome of 890 healthy Koreans and found that the gut microbiome composition differed from other countries, and was associated with age, dietary patterns, and other factors. The data obtained in this study provides valuable insights into the gut microbiome composition in healthy Korean population and its association with host health conditions.
Article
Microbiology
Miwei Lv, Jiawei Zhang, Jiaxin Deng, Jiancong Hu, Qinghua Zhong, Mingli Su, Dezheng Lin, Tian Xu, Xuhao Bai, Juan Li, Xuefeng Guo
Summary: This study aimed to analyze the differences in gut microbiome composition between adenoma and control populations. The results showed that Prevotella enterotype was only present in the adenoma group and was an independent risk factor for colorectal adenoma.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Xiaowu Bai, Yang Sun, Yue Li, Maojuan Li, Zhirui Cao, Ziyu Huang, Feng Zhang, Ping Yan, Lan Wang, Juan Luo, Jing Wu, Dejun Fan, Hongxia Chen, Min Zhi, Ping Lan, Zhong Zeng, Xiaojian Wu, Yinglei Miao, Tao Zuo
Summary: The composition of the gut archaeome is influenced by factors such as geography, urbanization, dietary habits, and ethnicity. Urbanization decreases the diversity and individual differences of the gut archaeome, as well as the abundance of Methanobrevibacter smithii in feces. M. smithii is correlated with several short chain fatty acid-producing bacteria in the gut, and a decreased abundance of M. smithii is associated with increased prevalence of noncommunicable diseases in urban populations.
Article
Multidisciplinary Sciences
Kihyun Lee, Sebastien Raguideau, Kimmo Siren, Francesco Asnicar, Fabio Cumbo, Falk Hildebrand, Nicola Segata, Chang-Jun Cha, Christopher Quince
Summary: The authors investigate the population-level impact of antimicrobial resistance genes (ARGs). By analyzing 8972 metagenomes and 3096 gut microbiomes from healthy individuals not taking antibiotics, they find significant correlations between the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Using a collection of 154,723 human-associated metagenome assembled genomes (MAGs), they link these ARGs to microbial taxa and detect horizontal gene transfer.
NATURE COMMUNICATIONS
(2023)
Article
Pediatrics
Miriam Aguilar-Lopez, Christine Wetzel, Alissa MacDonald, Thao T. B. Ho, Sharon M. Donovan
Summary: This study found that the gut microbiota of preterm infants is influenced by the type of feeding and fortification, and the growth of preterm infants is significantly associated with milk consumption and fortification methods.
FRONTIERS IN PEDIATRICS
(2021)
Article
Gastroenterology & Hepatology
Naoyoshi Nagata, Suguru Nishijima, Tohru Miyoshi-Akiyama, Yasushi Kojima, Moto Kimura, Ryo Aoki, Mitsuru Ohsugi, Kohjiro Ueki, Kuniko Miki, Eri Iwata, Kayoko Hayakawa, Norio Ohmagari, Shinichi Oka, Masashi Mizokami, Takao Itoi, Takashi Kawai, Naomi Uemura, Masahira Hattori
Summary: This study found that many drugs, including non-antibiotics, have an impact on the human gut microbiome, especially in individuals who are exposed to multiple drugs. Polypharmacy leads to changes in gut microbiome structure and microbial functions, as well as an increase in antimicrobial resistance potential. The initiation and cessation of drugs also cause alterations and recovery in the microbiome.
Article
Immunology
Lorena Ruiz, Claudio Alba, Cristina Garcia-Carral, Esther A. Jimenez, Kimberly A. Lackey, Michelle K. McGuire, Courtney L. Meehan, James Foster, Daniel W. Sellen, Elizabeth W. Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela K. Gindola, Gloria E. Otoo, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Janet E. Williams, Juan M. Rodriguez
Summary: This study reprocessed and resequenced a large set of human milk samples from diverse international sites, revealing the impact of different sequencing approaches on the microbiota profiles obtained for human milk samples and showing relatively consistent microbial configurations in the studied cohorts.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Environmental Sciences
Xueshu Li, Yanna Liu, Jonathan W. Martin, Julia Yue Cui, Hans-Joachim Lehmler
Summary: The gut microbiome plays an important role in the biotransformation of PCBs, impacting toxic outcomes following PCB exposure. This was evidenced through Nt-HRMS analysis of feces from mice exposed to PCB mixtures, showing differences in PCB metabolite levels between conventional and germ-free mice.
ENVIRONMENTAL POLLUTION
(2021)
Article
Microbiology
Sabine Schwarzer, Thomas Hackl, Hanna M. Oksanen, Tessa E. F. Quax
Summary: Viruses are highly diverse and abundant organisms that infect microorganisms, including archaea. Archaeal viruses have been less studied compared to viruses infecting bacteria and eukaryotes. In this study, researchers investigated the infection mechanism of archaeal virus HFTV1 and found that it binds to the cell wall component surface-layer protein for infection. Electron microscopy revealed that viral particles make direct contact with the cell surface, enhancing viral adsorption rates. This study provides insights into the entry mechanisms of archaeal viruses and expands our understanding of microbial viruses in general.
Article
Immunology
Epp Sepp, Imbi Smidt, Tiiu Roop, Jelena Stsepetova, Siiri Koljalg, Marika Mikelsaar, Indrek Soidla, Mare Ainsaar, Helgi Kolk, Mirjam Vallas, Madis Jaagura, Reet Mandar
Summary: This study compared the gut microbiota, living habits, and eating habits between centenarians and young people. The results showed that centenarians had a more diverse and abundant microbiota, with higher levels of hereditary and environmental microbes. Their childhood living conditions and diet differed from those of young people.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Hyun-Seok Oh, Uigi Min, Hyejin Jang, Namil Kim, Jeongmin Lim, Mauricio Chalita, Jongsik Chun
Summary: This study examines the human gut microbiota and proposes an index called GMI to consistently predict health conditions based on comprehensive comparative analysis of multiethnic data from various diseases.
JOURNAL OF MICROBIOLOGY
(2022)
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)
Article
Nutrition & Dietetics
Hye-Bin Lee, Moon-Ho Do, Hyunjhung Jhun, Sang-Keun Ha, Hye-Seon Song, Seong-Woon Roh, Won-Hyong Chung, Young-Do Nam, Ho-Young Park
Summary: Bacteroides uniformis CBA7346 ameliorates high-fat diet-induced non-alcoholic fatty liver disease by reducing insulin resistance and regulating de novo lipogenesis.
Article
Microbiology
Eui-Sang Cho, In-Tae Cha, Seong Woon Roh, Myung-Ji Seo
Summary: Three novel halophilic archaea, isolated from seawater and sediment near Yeoungheungdo Island in Korea, belong to the genus Haloferax, with similarities and differences in their genetic properties. They thrive in high-salt environments and exhibit specific physiological and metabolic characteristics.
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
Juseok Kim, Hye Seon Song, Joon Yong Kim, Tae Woong Whon, Won-Hyong Chung, Young -Do Nam, Yoon-E Choi, Seong Woon Roh
Summary: A novel bacterial strain, CBA7301T, was isolated from human faeces and identified as a member of the genus Bacteroides. It showed 96.2% similarity in 16S rRNA gene sequence with its closest related species, Bacteroides faecichinchillae JCM 17102T. CBA7301T is a Gram-stain-negative, strictly anaerobic, rod-shaped bacterium that grows optimally at 30-35°C, pH 7.0, and 0.5% NaCl.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(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)