Article
Biochemical Research Methods
Tang Li, Yanbin Yin
Summary: The pan-genome analysis of metagenome-assembled genomes (MAGs) can be affected by issues such as fragmentation, incompleteness, and contamination. In this study, the researchers conducted a critical assessment of pan-genomics by comparing the results of complete bacterial genomes and simulated MAGs. The findings show that incompleteness leads to significant loss of core genes, while contamination mainly affects accessory genomes. Lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes can alleviate the loss, but to a limited extent. The study concludes that new pan-genome analysis tools specifically for MAGs are needed.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Francesca Petriglieri, Caitlin M. Singleton, Zivile Kondrotaite, Morten K. D. Dueholm, Elizabeth A. McDaniel, Katherine D. McMahon, Per H. Nielsen
Summary: Candidatus Accumulibacter is an important polyphosphate-accumulating organism (PAO) in wastewater phosphorus removal. However, its taxonomic classification at the species level is complicated. This study provides a comprehensive reassessment of the phylogeny using genome, ppk1, and 16S rRNA gene-based approaches, resulting in the identification of novel species and clarification of the taxonomy. Additionally, the metabolic capabilities of Candidatus Accumulibacter species were explored using genome mining and in situ validation, providing insights into their niche differentiation and contribution to nutrient removal.
Article
Microbiology
Nitin K. Singh, Jason M. Wood, Jose Patane, Livia Maria Silva Moura, Jonathan Lombardino, Joao Carlos Setubal, Kasthuri Venkateswaran
Summary: In this study, metagenome-assembled genomes (MAGs) were generated to analyze the microbial diversity and functional properties of the International Space Station (ISS) environment. The results showed that ISS samples contained 18 bacterial species and 4 fungal genomes. The study revealed evolution of microbes in space, enrichment of genes related to cell membranes, and higher prevalence of antimicrobial resistance and virulence genes in certain bacteria. Comparative analysis indicated that Pantoea/Kalamiella strains are more susceptible to microgravity changes. These findings contribute to understanding microbial evolution under microgravity and radiation pressure.
Article
Genetics & Heredity
Jie Zhu, Liu Tian, Peishan Chen, Mo Han, Liju Song, Xin Tong, Xiaohuan Sun, Fangming Yang, Zhipeng Lin, Xing Liu, Chuan Liu, Xiaohan Wang, Yuxiang Lin, Kaiye Cai, Yong Hou, Xun Xu, Huanming Yang, Jian Wang, Karsten Kristiansen, Liang Xiao, Tao Zhang, Huijue Jia, Zhuye Jie
Summary: By analyzing a large number of oral metagenomic samples, researchers obtained a comprehensive collection of oral microbial genomes. These genomes provide valuable insights into the potential drug metabolism and disease diagnosis capabilities of oral microbes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Christen L. Grettenberger, Trinity L. Hamilton
Summary: Metagenome-assembled genomes from novel AMD taxa provide insights into key taxa involved in carbon, nitrogen, sulfur, and iron cycling in AMD environments. These data are important for understanding biogeochemical cycling in AMD environments and can inform bioremediation strategies.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Carlos A. Ruiz-Perez, Anthony D. Bertagnolli, Despina Tsementzi, Tanja Woyke, Frank J. Stewart, Konstantinos T. Konstantinidis
Summary: The diverse and ubiquitous members of the SAR11 lineage, particularly two subclades associated with mesopelagic and oxygen minimum zone environments, show similarities in central carbon metabolism with some variations, suggesting unique functional versatility in mesopelagic-adapted clades. Genomic analyses led to the proposal of two new SAR11 genera specifically adapted to mesopelagic and OMZ environments.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Microbiology
Zhen-Hao Luo, Manik Prabhu Narsing Rao, Hao Chen, Zheng-Shuang Hua, Qi Li, Brian P. Hedlund, Zhou-Yan Dong, Bing-Bing Liu, Shu-Xian Guo, Wen-Sheng Shu, Wen-Jun Li
Summary: The study employed a metagenomics approach to obtain MAGs of Candidatus Nitrosocaldaceae from hot spring samples in India and China, revealing new species and a novel genus. Key genes responsible for chemolithotrophic ammonia oxidation and a thaumarchaeal 3HP/4HB cycle were detected in all MAGs, along with genes related to thermal adaptation and interactions with archaea and bacteria.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Baoyu Xiang, Liping Zhao, Menghui Zhang
Summary: In this study, a new approach called UGMAGrefiner was proposed, which utilizes the connection and coverage information from unitig level assembly graphs to improve the quality of metagenome-assembled genomes (MAGs). UGMAGrefiner outperforms state-of-the-art binning refine tools and can identify genome specific regions of mixed genomes. It provides an efficient way to obtain more complete MAGs and study genome specific functions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Food Science & Technology
Aitor Balmaseda, Marc Lorentzen, Lucie Dutilh, Remi Bauduin, Hugues Guichard, Severine Ollivier, Cecile Miot-Sertier, Patrick M. Lucas
Summary: O. oeni is the main lactic acid bacteria species in wine and cider, responsible for malo-lactic fermentation. The majority of strains in wine belong to phylogroups A, B + C, and D, while in cider, A, B, and C strains are dominant. Ethanol and fermentation kinetics drive the selection of phylogroup A strains in wine, while B and C strains dominate in cider with lower ethanol content.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Varsha Bohra, Hitesh Tikariha, Hemant J. Purohit, Nishant A. Dafale
Summary: This study reconstructed genomes from environmental metagenomes sourced from cow and buffalo rumen, assembling 12 high-quality metagenome-assembled genomes (MAGs) with high novelty. The genomes contained a significant number of unannotated carbohydrate-active enzymes (CAZymes) and plant biomass degrading genes.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Bakshi Amulyasai, Rai Anusha, Chintalapati Sasikala, Chintalapati Venkata Ramana
Summary: Three metagenome-assembled genomes were constructed from a sediment sample, and one genome (Bin1, JB001) was identified as a bacterium belonging to the purple sulfur bacteria group with photosynthetic abilities and the capability to fix nitrogen and tolerate salt.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Immunology
Zhongdong Lv, Yong Chen, Houqing Zhou, Zhonglin Chen, Qianru Yao, Jiali Ren, Xianglu Liu, Shuang Liu, Xiaomei Deng, Yingchen Pang, Weijun Chen, Huiling Yang, Ping Xu
Summary: Whipple's disease is a rare chronic systemic disease caused by the intracellular bacterium Tropheryma whipplei. It can affect almost any organ system of the body. By studying the genomes of two T. whipplei strains from China, it was found that geographic origins cannot explain the phylogenetic relationships among different strains. Additionally, T. whipplei has a closed genome, is resistant to fluoroquinolones, and shares the same virulence factors.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Nikolai V. Ravin, Tatyana S. Rudenko, Dmitry D. Smolyakov, Alexey V. Beletsky, Andrey L. Rakitin, Nikita D. Markov, Alexey Fomenkov, Luo Sun, Richard J. Roberts, Andrey A. Novikov, Olga V. Karnachuk, Margarita Y. Grabovich
Summary: Two strains of filamentous, colorless sulfur bacteria were isolated from a coal mine and the White Sea, while a metagenome-assembled genome was obtained from a sulfidic spring in Russia. Phylogenetic analysis showed that all genomes belonged to the genus Thiothrix, with three proposed new species identified. The core genome of Thiothrix includes genes for metabolism, respiration, and sulfur oxidation pathways.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Vicente Gomez-Alvarez, Sallamaari Siponen, Ari Kauppinen, Anna-Maria Hokajarvi, Ananda Tiwari, Anniina Sarekoski, Ilkka T. Miettinen, Eila Torvinen, Tarja Pitkanen
Summary: The study used next-generation sequencing technologies to analyze the water microbiome in five waterworks in Finland. The presence and type of disinfectant residual exert selective pressure on the microbial community. The microbial community in non-disinfected drinking water systems is important and maintaining disinfectant residual is crucial for reducing microbial numbers and diversity.
Article
Food Science & Technology
Pynhunlang Kharnaior, Jyoti Prakash Tamang
Summary: This study investigated the microbiome, metabolites, and metagenome-assembled genomes (MAGs) of four fermented soybean foods made by the native people of Arunachal Pradesh. The study found that bacteria dominated the microbiome, with lactobacilli being the most abundant. The metabolomics analysis revealed targeted and untargeted metabolites involved in flavor development and therapeutic properties. High-quality MAGs of certain species showed biomarkers associated with various bio-functional properties. The study also provided insights into the cultivability of these MAGs for future use as starter cultures in fermented soybean food production. Additionally, a comparison with other fermented soybean foods in Asia showed distinct differences in microbiome and metabolites.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Review
Food Science & Technology
Luc De Vuyst, Andrea Comasio, Simon Van Kerrebroeck
Summary: This article reviews the fermentation strategies and microbial ecology of sourdough production, with a focus on non-flour ingredients. Different types of sourdough production are classified based on the inoculum used. Traditional recipes for Type 1 sourdough often include non-flour ingredients as a microbial inoculum source or fermentation substrates.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Biotechnology & Applied Microbiology
David Van der Veken, Charlie Hollanders, Marko Verce, Chris Michiels, Steven Ballet, Stefan Weckx, Frederic Leroy
Summary: The analysis of the genome of Mammaliicoccus sciuri IMDO-S72 has revealed the genetic mechanisms behind its antibacterial phenotype and provided insights into the potential virulence factors of this species. The presence of a plasmid-encoded gene cluster responsible for antimicrobial activity, as well as the identification of micrococcin P1 as the compound produced, were significant findings. The genome also showed the presence of innate virulence factors and antibiotic resistance genes, although their consistent link to a resistance phenotype was not observed. Importantly, this study highlights the commensal lifestyle of M. sciuri and the role of mobile genetic elements in conferring antibiotic resistance.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
E. Duthoo, K. De Reu, F. Leroy, S. Weckx, M. Heyndrickx, G. Rasschaert
Summary: The composition and dynamics of the microbiota present on vegetarian alternative to poultry-based charcuterie during storage were investigated using both culture-dependent and culture-independent methods. Lactic acid bacteria were found to be the most abundant microbial group, while the presence of Xanthomonas DNA was likely due to the use of xanthan gum as an ingredient.
Review
Biotechnology & Applied Microbiology
Cristian Diaz-Munoz, Luc De Vuyst
Summary: The application of starter culture mixture in cocoa fermentation plays a crucial role in improving the quality and flavor of chocolate products, making it essential to select appropriate strains for the process.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Cristian Diaz-Munoz, Dario Van de Voorde, Emmy Tuenter, Valerie Lemarcq, Davy Van de Walle, Jose Pedro Soares Maio, Alejandra Mencia, Carlos Eduardo Hernandez, Andrea Comasio, Eleni Sioriki, Stefan Weckx, Luc Pieters, Koen Dewettinck, Luc De Vuyst
Summary: This study examined the effects of Hanseniaspora opuntiae strain in cocoa fermentation. The results showed that the inoculated H. opuntiae strain was unable to dominate over other yeasts, resulting in under-fermented cocoa beans. However, cocoa fermentation processes inoculated with Saccharomyces cerevisiae strain produced richer and more reproducible aroma profiles.
Article
Multidisciplinary Sciences
Cristian Diaz-Munoz, Marko Verce, Luc De Vuyst, Stefan Weckx
Summary: This study unraveled the genome of the cocoa strain S. cerevisiae IMDO 050523 and found its close genetic relationship with a West African fermented food population. It also identified genetic signatures related to sucrose hydrolysis, pectin degradation, osmotolerance, and ester-producing enzymes, suggesting specific niche adaptations.
Article
Microbiology
Rudy Pelicaen, Stefan Weckx, Didier Gonze, Luc De Vuyst
Summary: In this study, a comparative genomic analysis was conducted on two candidate starter culture strains for cocoa fermentation, A. ghanensis LMG 23848(T) and A. senegalensis 108B, using genome sequence data. Genome-scale metabolic models (GEMs) were reconstructed to gain insights into their metabolic adaptations. The analysis revealed differences in carbon core metabolism and redox metabolism among Acetobacter species, providing new insights into cocoa fermentation and potential guidelines for future research.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Louise Vermote, Jonas De Roos, Margo Cnockaert, Peter Vandamme, Stefan Weckx, Luc De Vuyst
Summary: Belgian lambic beers are produced using traditional craftsmanship, relying on wooden barrels for spontaneous fermentation and maturation. These barrels play a crucial role in establishing a stable microbial ecosystem, minimizing batch-to-batch variations, and preventing flavor deviations. They provide an inoculation source of necessary microorganisms and a microaerobic environment for successful lambic beer production.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Microbiology
Hannes Decadt, Stefan Weckx, Luc De Vuyst
Summary: This study evaluated the impact of three different starter culture mixtures on the organoleptic properties of Gouda cheeses. Analysis of 23 batches of cheeses at different ripening times revealed that different starter cultures led to variations in key metabolite concentrations and the relative abundance of non-starter lactic acid bacteria. Leuconostoc pseudomesenteroides played a minor role in aroma formation but had a major impact on the growth of non-starter lactic acid bacteria. The relative abundance of Tetragenococcus halophilus (high) and Loigolactobacillus rennini (low) increased from the rind to the core with ripening time, suggesting that a well-chosen T. halophilus strain could be used as an adjunct culture for Gouda cheese production.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Food Science & Technology
Celine Verdonck, Yamina De Bondt, Ines Pradal, An Bautil, Niels A. Langenaeken, Kristof Brijs, Peter Goos, Luc De Vuyst, Christophe M. Courtin
Summary: The final quality of wholemeal wheat bread is influenced by process parameter settings and leavening strategy. This study found that the specific volume of bread varied depending on the type of leavening strategy used, with a lower specific volume observed with sourdough compared to baker's yeast. The proofing time and water absorption had different effects on the specific volume when using different leavening strategies.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Plant Sciences
Ramon de Koning, Gertjan E. Wils, Raphael Kiekens, Luc De Vuyst, Geert Angenon
Summary: Due to climate change, farmers will face more extreme weather conditions and hence will need crops that are better adapted to these challenges. This study presents new insights into the role of raffinose family oligosaccharides (RFOs) as a resilience mechanism against environmental stress in common bean, particularly focusing on galactinol and RFOs in common beans exposed to drought and salt stress conditions.
Article
Biotechnology & Applied Microbiology
Lihan Huang, Nurul Hawa Ahmad, Vijay Juneja, Erika Stapp-Kamotani, Jose Gabiola, Udit Minocha, Robert Phillips, Marie Hooker, Isabel Walls, Kim Cook, James Lindsay
Summary: This study investigated the growth kinetics of foodborne pathogen B. cereus during the commercial production of liquid egg yolk using PLA(2) treatment. The results showed that B. cytotoxicus NVH391-98 can grow prolifically at 50 degrees C, with estimated minimum, optimum, and maximum temperatures of 16.7-18.5, 47.8-48.1, and 52.1-52.4 degrees C, respectively. The dynamic model was validated with isothermal curves and it was found that holding the temperature below 15 degrees C or above 55 degrees C can effectively prevent the growth of B. cytotoxicus in egg yolk.
Article
Biotechnology & Applied Microbiology
Giacomo Mantegazza, Robin Duncan, Nicolo Telesca, Giorgio Gargari, Susanna Perotti, Patrizia Riso, Simone Guglielmetti
Summary: This study investigates whether salad-associated LAB can survive the gastrointestinal transit (GIT) and contribute to the gut microbiota. The results suggest that salad-associated LAB can survive in the gastrointestinal tract, but their quantity does not significantly alter the composition of the gut microbiota.
Article
Biotechnology & Applied Microbiology
Itsaso Baztarrika, Adrian Salazar-Sanchez, Lorena Laorden, Ilargi Martinez-Ballesteros, Rodrigo Alonso, Irati Martinez-Malaxetxebarria
Summary: The infection mechanisms of Arcobacter are still uncertain. This study found that Arcobacter isolates from food and water sources were able to adhere and invade Caco-2 cells, and carried at least two virulence markers. A. butzleri showed higher virulent activity compared to A. cryaerophilus, while A. lanthieri, A. skirrowii, and A. vitoriensis exhibited even higher adhesion and invasion values. Sewage isolates were more adherent and invasive, and had a higher gene content. The association between cadF and hecA with high adhesion capability was identified for the first time.
Article
Biotechnology & Applied Microbiology
Balaji Sundararaman, Karen Shapiro, Andrea Packham, Lauren E. Camp, Rachel S. Meyer, Beth Shapiro, Richard E. Green
Summary: Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases, and surveillance methods are needed. In this study, CNER method was used to prepare enrichment baits for difficult-to-grow pathogens. This method allows direct sequencing of pathogens from samples.
Article
Biotechnology & Applied Microbiology
Guanghui Zhou, Pengcheng Dong, Xin Luo, Lixian Zhu, Yanwei Mao, Yunge Liu, Yimin Zhang
Summary: Interactions between bacterial species in the formation of dual-species biofilms in the food industry are affected by environmental stresses, such as temperature and pH. This study found that the combination of cold and acid stresses significantly increased biofilm formation, and different temperatures resulted in variations in the presence of specific bacterial species and the secretion of extracellular substances. The findings provide valuable insights for addressing mixed biofilms in food processing under diverse stressful conditions.
Article
Biotechnology & Applied Microbiology
Carmen Sanchez, Sonia Garde, Jose Maria Landete, Javier Calzada, Dave J. Baker, Rhiannon Evans, Arjan Narbad, Melinda J. Mayer, Marta Avila
Summary: This study sequenced and compared the genomes of bacteriophages active against C. tyrobutyricum, identifying novel species and phage proteins. A phage showed high lytic activity against C. tyrobutyricum cells and remained stable under different environmental conditions. Additionally, engineered strains successfully delivered endolysin and fluorescent protein to dairy products without affecting their technological properties.
Article
Biotechnology & Applied Microbiology
Danai Etter, Michael Biggel, Mariella Greutmann, Nicole Cernela, Sophia Johler
Summary: Bacillus cytotoxicus is a thermotolerant bacterium that is linked to rare but sometimes fatal cases of diarrheal disease. It is mostly found in dehydrated foods containing potato starch or insects and may be missed in routine screening.
Article
Biotechnology & Applied Microbiology
Tong Jin, Xiangjun Zhan, Liuxin Pang, Bo Peng, Xinpeng Zhang, Wenxiu Zhu, Baowei Yang, Xiaodong Xia
Summary: The study found that CpxAR TCS is an important regulatory mechanism for the virulence of C. sakazakii. Mutants showed weakened adhesion, invasion, and survival ability, and exhibited attenuated virulence in animal models. In addition, CpxAR TCS is involved in regulating the expression of genes associated with bacterial virulence and cellular invasion.
Article
Biotechnology & Applied Microbiology
Soo-Hwan Kim, Sang-Hyun Park, Jun-Bae Ahn, Dong-Hyun Kang
Summary: In this study, a semi continuous SHS system was developed to inactivate foodborne pathogens on radish seed surfaces and enhance the seeds' salinity tolerance. The results showed that higher temperature and more treatments led to a significant reduction in microbial count on the seed surface.
Article
Biotechnology & Applied Microbiology
Yujun Zhai, Weina Tian, Kewei Chen, Linshu Lan, Jianquan Kan, Hui Shi
Summary: This research investigates the role of flagella-related genes in the adhesion of E. coli O157:H7 and the effects of certain cations on bacterial adhesion and motility. The results demonstrate that flagellar-mediated motility is critical in the early stage of adhesion, and the presence of Fe2+, Ca2+, and Mn2+ affects the adhesion and motility of wildtype strains but not flagellar function-impaired strains. These findings provide new insights into the mechanisms of bacterial adhesion and have implications for the development of anti-adhesion agents.
Article
Biotechnology & Applied Microbiology
Mariana Marggraf, Andrea Barac, Jens Andre Hammerl, Stefan Hertwig
Summary: Isolating Yersinia enterocolitica from food is challenging due to overgrowth by other microflora and the lack of a selective medium. The authors improved the standard isolation procedure, resulting in a more sensitive method, reduced background bacteria, and time savings.
Article
Biotechnology & Applied Microbiology
Rafael D. Chaves, Samuel H. Kumazawa, Amin Mousavi Khaneghah, Veronica O. Alvarenga, Humberto M. Hungaro, Anderson S. Sant'Ana
Summary: This study investigated the susceptibility to sanitizers and biofilm-forming ability of 43 Salmonella enterica and Listeria monocytogenes strains on stainless steel surfaces. The results showed variations in susceptibility to sanitizers and biofilm resistance among different strains of the pathogens, with chlorine compounds being more effective in inactivating planktonic cells and biofilms.
Article
Biotechnology & Applied Microbiology
So Yeong Mun, Wooje Lee, Soo-Young Lee, Ji Yoon Chang, Hae Choon Chang
Summary: This study reveals that lactobacilli with a strong defense system dominate the final stage of kimchi fermentation and proposes a model for the succession mechanism of kimchi lactobacilli.
