Article
Genetics & Heredity
Ruilin Lai, Min Lin, Yongliang Yan, Shijie Jiang, Zhengfu Zhou, Jin Wang
Summary: The genus Geobacillus contains thermophilic gram-positive bacteria with wide distribution and high temperature tolerance, making them suitable for various biotechnology and industrial applications. In this study, the genome of Geobacillus stearothermophilus H6 was sequenced and analyzed, and the thermophilic enzyme in the strain was identified. The results could contribute to the development and application of industrial strains.
Article
Microbiology
Donglin Ma, Shuangping Liu, Xiao Han, Mujia Nan, Yuezheng Xu, Bin Qian, Lan Wang, Jian Mao
Summary: This study investigated the functions and application of Saccharopolyspora rosea (S. rosea) A22 in the fermentation process of huangjiu. The whole genome sequencing and functional genomic analysis revealed its regulatory mechanisms under harsh conditions and a genome-scale metabolic model was constructed. The experimental results showed that this strain could reduce the total higher alcohol content during huangjiu fermentation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sadia Mehmood Satti, Edgar Castro-Aguirre, Aamer Ali Shah, Terence L. Marsh, Rafael Auras
Summary: The genomes of Pseudomonas aeruginosa S3, Sphingobacterium S2, and Geobacillus EC-3, isolated from compost, were annotated to understand their ability to degrade poly(lactic acid) (PLA). The draft genomes revealed catabolic genes for biodegradation of xenobiotics, aromatic compounds, and lactic acid, as well as genes related to biofilm formation and regulation. These isolates possess essential genetic elements for PLA metabolism at both mesophilic and thermophilic temperatures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Virology
Joe Tang, Catia Delmiglio, Lisa Ward, Jeremy Thompson
Summary: A new virus, named sweetbriar rose curly-top associated virus (SRCTaV), was identified in sweetbriar rose using high-throughput sequencing. The complete genome sequence of SRCTaV was determined and characterized. Phylogenetic analysis revealed that SRCTaV is closely related to members of the genus Waikavirus.
ARCHIVES OF VIROLOGY
(2022)
Article
Plant Sciences
Zhengying Cao, Linyi Yang, Yaxuan Xin, Wenbin Xu, Qishao Li, Haorong Zhang, Yuxiang Tu, Yu Song, Peiyao Xin
Summary: This study conducted comparative genomic and phylogenetic analyses on seven Neocinnamomum taxa, revealing the genetic structure and evolutionary characteristics of these species. The chloroplast genome of Neocinnamomum has a size range of 150,753-150,956 bp and contains 128 annotated genes. The study identified 31 preferred codons and three highly variable regions. The results of this study will serve as a reference for molecular marker development and phylogenetic research in Neocinnamomum.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Virology
Caterynne Melo Kauffmann, Alessandra de Jesus Boari, Joao Marcos Fagundes Silva, Rosana Blawid, Tatsuya Nagata
Summary: A cytorhabdovirus, tentatively named patchouli chlorosis-associated cytorhabdovirus (PCaCV), was identified in a patchouli plant using high-throughput sequencing. The genome sequence of PCaCV was confirmed and found to contain six open reading frames. PCaCV is most closely related to tomato yellow mottle-associated virus and should be considered a new member of the genus Cytorhabdovirus.
ARCHIVES OF VIROLOGY
(2022)
Article
Virology
Rachelle Bester, Leonidas Lotos, Abraham Vermeulen, Gerhard Pietersen, Varvara I. Maliogka, Hans J. Maree
Summary: High-throughput sequencing was utilized to analyze the virome profile of a grapevine infected with grapevine leafroll disease, revealing a virus sequence similar to those of the genus Badnavirus. The complete genome sequence of this virus, a divergent variant of grapevine Roditis leaf discoloration-associated virus (GRLDaV), was identified with 90% nucleotide sequence identity to an isolate from South African variant.
ARCHIVES OF VIROLOGY
(2021)
Article
Virology
Weizhong Chang, Xiaoli Jiao, Hongyan Sui, Suranjana Goswami, Brad T. Sherman, Caroline Fromont, Juan Manuel Caravaca, Bao Tran, Tomozumi Imamichi
Summary: This study assembled and annotated the complete genome of HSV-2 strain G using PacBio long sequencing reads. It analyzed the 'alpha' sequence and identified packaging signals homologous to HSV-1, as well as determined the termini and cleavage site of the linear genome. The study also visualized four HSV-2 genome isomers using Oxford Nanopore Technology sequencing reads. Additionally, the coding sequences of strain G were compared with other HSV-2 strains and a phylogenetic analysis was conducted.
Article
Biotechnology & Applied Microbiology
Dummi Mahadevan Gurumurthy, Muhammad Bilal, Ashok Kumar Nadda, Vaddi Damodara Reddy, Ganesh Dattatraya Saratale, Urszula Guzik, Luiz Fernando Romanholo Ferreira, Sanjay Kumar Gupta, Mohammed Azharuddin Savanur, Sikandar I. Mulla
Summary: This study identified a cell wall-associated extracellular electron transfer (EET) in the thermophilic Geobacillus sp. for utilizing iron as a terminal electron acceptor. The transfer of electrons was primarily linked to cell wall cytochrome-c and diffusible redox mediators during anoxic conditions. The study suggests that the absence of surface polysaccharide and diffusible mediators favors the cell wall-associated EET pathway in Geobacillus sp.
Article
Multidisciplinary Sciences
Xin Jie Ching, Nazalan Najimudin, Yoke Kqueen Cheah, Clemente Michael Vui Ling Wong
Summary: Here, we report the complete genome sequence of Parageobacillus caldoxylosilyticus ER4B isolated from empty oil palm fruit bunch compost in Malaysia. The genome size of ER4B strain was approximately 3.9Mbp with a GC content of 44.31%. This study provides molecular information and insights into the adaptation of bacteria to extreme temperatures.
Article
Microbiology
Chinda Chhe, Ayaka Uke, Sirilak Baramee, Chakrit Tachaapaikoon, Patthra Pason, Rattiya Waeonukul, Khanok Ratanakhanokchai, Akihiko Kosugi
Summary: We isolated and analysed a thermophilic bacterium, strain DA-C8(T), from compost in Ishigaki Island, Japan, that can degrade xylan and other polysaccharides. The strain showed high xylan degradation ability under anaerobic growth conditions, with an optimum growth temperature of 55 degrees C and pH 9.0. Phylogenetic analysis revealed that strain DA-C8(T) belongs to the proposed novel genus Insulambacter gen. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Agronomy
Xiaoyan Li, Qiuju Han, Mengyao Li, Qing Luo, Shunhua Zhu, Yangxia Zheng, Guofei Tan
Summary: In this study, the mitochondrial genome of watercress was assembled using Illumina and Nanopore sequencing platforms, revealing a circular structure of 384,074 bp with 28 tRNA genes, 3 rRNA genes, and 34 protein-coding genes. The study also identified watercress's codon preference for leucine, isoleucine, and serine, and its close evolutionary relationship with species such as Bupleurum, Apium, Angelica, and Daucus. This research provides a valuable resource for the study of watercress evolution and molecular breeding.
Article
Plant Sciences
Zhaohui Lan, Yuhua Shi, Qinggang Yin, Ranran Gao, Chunlian Liu, Wenting Wang, Xufang Tian, Jiawei Liu, Yiying Nong, Li Xiang, Lan Wu
Summary: This study analyzed the chloroplast genomes of five Artemisia species and identified four highly variable regions that can be used as molecular markers for species identification. Phylogenetic analysis showed close relations between the investigated species. The study suggests that the chloroplast genome can serve as a universal super barcode for plant identification.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Zhengying Cao, Wenzhi Zhao, Yaxuan Xin, Weixiang Shen, Fei Wang, Qishao Li, Yuxiang Tu, Haorong Zhang, Zhanghong Dong, Peiyao Xin
Summary: This study explored the genetic structure and evolutionary characteristics of the chloroplast genome of Pourthiaea using comparative genomics and phylogenetic analysis. The results showed that the chloroplast genomes of Pourthiaea species were conserved with some variation in spacer regions. Phylogenetic analysis revealed a close relationship between Pourthiaea and Stranvaesia genus. The findings provide valuable insights for breeding, genetic evolution, and phylogeny of Pourthiaea.
Article
Biotechnology & Applied Microbiology
Yonggang Qiao, Xinrui Zhang, Zheng Li, Yun Song, Zhe Sun
Summary: In this study, the mitochondrial genome of Bupleurum chinense was assembled and annotated. The results provide extensive information about the characteristics of the mitochondrial genome and lay the foundation for future studies on genetic variations, phylogeny, and breeding in B. chinense.
Review
Food Science & Technology
Jyoti Prakash Tamang, Paul D. Cotter, Akihito Endo, Nam Soo Han, Remco Kort, Shao Quan Liu, Baltasar Mayo, Nieke Westerik, Robert Hutkins
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2020)
Article
Microbiology
Alex Paul Wacoo, Prudence Atukunda, Grace Muhoozi, Martin Braster, Marijke Wagner, Tim J. van den Broek, Wilbert Sybesma, Ane C. Westerberg, Per Ole Iversen, Remco Kort
Editorial Material
Pediatrics
Per O. Iversen, Prudence Atukunda, Remco Kort, Per M. Ueland, Ane C. Westerberg, Grace K. M. Muhoozi
Editorial Material
Public, Environmental & Occupational Health
Gregor Reid, Wilbert Sybesma, William Matovu, Arnold Onyango, Nieke Westerik, Remco Kort
JOURNAL OF GLOBAL HEALTH
(2020)
Article
Nutrition & Dietetics
Nieke Westerik, Arinda Nelson, Alex Paul Wacoo, Wilbert Sybesma, Remco Kort
FRONTIERS IN NUTRITION
(2020)
Article
Microbiology
Simon Syvertsson, Biwen Wang, Jojet Staal, Yongqiang Gao, Remco Kort, Leendert W. Hamoen
Summary: Bacteria can adapt to environmental changes through bimodal differentiation, resulting in different cell types within a population. Study on Bacillus subtilis revealed that motile cells express less ribosomal genes, with resources being redirected to chemotaxis and motility systems during exponential growth. This growth rate reduction in motile cells contributes to the bimodal induction of motility.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Scarlett Puebla-Barragan, Emiley Watson, Charlotte van der Veer, John A. Chmiel, Charles Carr, Jeremy P. Burton, Mark Sumarah, Remco Kort, Gregor Reid
Summary: The study found that different strains of Lactobacillus crispatus in the vagina can produce or degrade different biogenic amines, leading to varying effects on vaginal pH and pathogens. Additionally, strains isolated from women with dysbiotic vaginal microbiota showed stronger antimicrobial effects against certain pathogens.
Article
Endocrinology & Metabolism
Bonnie E. Brett, Bruno K. Koko, Habib O. Y. Doumbia, Frederic Kouadio Koffi, Savorgnan E. Assa, Kollet Y. A. S. Zahe, Hortense Faye-Kette, Seraphin Kati-Coulibaly, Remco Kort, Wilbert Sybesma, Gregor Reid, Carolina de Weerth
Summary: In economically-disadvantaged young children, a probiotic food supplement may lower cortisol levels, while CRP levels remain relatively unaffected. Further research on the impact of dose and regularity of consumption is warranted.
PSYCHONEUROENDOCRINOLOGY
(2021)
Article
Microbiology
Remco Kort, Job Schlosser, Alan R. Vazquez, Prudence Atukunda, Grace K. M. Muhoozi, Alex Paul Wacoo, Wilbert F. H. Sybesma, Ane C. Westerberg, Per Ole Iversen, Eric D. Schoen
Summary: The study investigated the association between gut microbiota composition and language development in 3-year-old rural Ugandan children. Using a novel regress methodology, it was found that the abundance of the anaerobic butyrate-producing gut bacterium Coprococcus eutactus is correlated with language development. The presence of oxygen tolerant species in the gut microbiota may also be linked to language impairment.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Susan L. Prescott, Ganesa Wegienka, Remco Kort, David H. Nelson, Sabine Gabrysch, Trevor Hancock, Anita Kozyrskyj, Christopher A. Lowry, Nicole Redvers, Blake Poland, Jake Robinson, Jean-Claude Moubarac, Sara Warber, Janet Jansson, Aki Sinkkonen, John Penders, Susan Erdman, Ralph Nanan, Matilda van den Bosch, Kirk Schneider, Nicholas J. Schroeck, Tanja Sobko, Jamie Harvie, George A. Kaplan, Rob Moodie, Laura Lengnick, Isaac Prilleltensky, Yuria Celidwen, Susan H. Berman, Alan C. Logan, Brian Berman
Summary: The Earthrise photograph from 1968 Apollo 8 mission sparked environmental awareness and human unity, leading to the first Earth Day in 1970. 50 years later, Project Earthrise is building on the concept of planetary health to address global challenges and promote collaborative action for personal, environmental, economic, and societal health.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Biochemistry & Molecular Biology
Rosanne Hertzberger, Ali May, Gertjan Kramer, Isabelle van Vondelen, Douwe Molenaar, Remco Kort
Summary: Glycogen in the female lower reproductive tract is an important carbon source for colonization and acidification by vaginal Lactobacillus crispatus. This study characterizes the genetic variation and regulation of the pulA gene, which correlates with the ability to utilize glycogen for growth. The findings suggest that environmental and genetic factors contribute to the variation of Lactobacillus crispatus alpha-glucosidases in the vaginal environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ton Baars, Betty van Esch, Luuk van Ooijen, Zuomin Zhang, Pieter Dekker, Sjef Boeren, Mara Diks, Johan Garssen, Kasper Hettinga, Remco Kort
Summary: This study aimed to characterize the microbiota and peptidomic composition of raw milk kefir and investigate its potential anti-allergic effects using validated research models for food allergy. The raw milk kefir was produced with a defined freeze-dried starter culture, and samples were taken during fermentation at seven time intervals. Peptide compositions were analyzed in the raw and heat-treated milk, as well as the kefir products made from these milks. The results showed that only raw milk kefir suppressed the acute allergic skin response in sensitized mice, indicating its potential health benefits.
Article
Multidisciplinary Sciences
Bonnie E. Brett, Habib O. Y. Doumbia, Bruno K. Koko, Frederic Kouadio Koffi, Savorgnan E. Assa, Kollet Y. A. S. Zahe, Remco Kort, Wilbert Sybesma, Gregor Reid, Carolina de Weerth
Summary: Despite the risk of children in low- and middle-income countries not reaching their full developmental potential, cognitive skills critical for success have mostly been studied in Western populations. This semi-randomized controlled trial examined normative cognitive development in 251 4- to 7-year-old children in urban schools in Cote d'Ivoire and explored the potential of enhancing cognition through probiotic consumption.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Scarlett Puebla-Barragan, Polycronis Paul Akouris, Kait F. Al, Charles Carr, Britney Lamb, Mark Sumarah, Charlotte van der Veer, Remco Kort, Jeremy Burton, Gregor Reid
Summary: The study found that certain Lactobacillus strains could reduce the malodorous compounds BAs, and cadaverine was found to reduce the relative abundance of lactobacilli. In an acidic environment, the growth of Lactobacillus species was enhanced, highlighting the importance of maintaining an acidic vaginal environment for vaginal health.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Food Science & Technology
Ivan Muzira Mukisa, Stellah Byakika, Rehema Meeme, Alex Paul Wacoo, Wilbert Sybesma, Remco Kort
NUTRITION & FOOD SCIENCE
(2020)
