Article
Veterinary Sciences
Abdallah A. Hassanin, Ali Osman, Osama Osman Atallah, Mohamed T. El-Saadony, Sameh A. Abdelnour, Heba S. A. Taha, Mohamed F. Awad, Hany Elkashef, Ahmed Ezzat Ahmed, Ibrahim Abd El-Rahim, Abdullah Mohamed, Ahmed S. Eldomiaty
Summary: This study analyzed the characteristics and properties of caseins in different dairy animals using bioinformatics methods. The results showed that caseins from different animals have different sequences and chemical properties, which have significant implications for the quality and functionality of milk products.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Microbiology
Rene L. Hoover, Jessica L. Keffer, Shawn W. Polson, Clara S. Chan
Summary: The pangenomic analysis of Gallionellaceae revealed a diverse genomic potential, with the presence of both iron-oxidizing bacteria and nitrite-oxidizing bacteria. Iron-oxidizing bacteria have a range of adaptations and mechanisms for extracellular electron uptake, enabling them to efficiently oxidize iron as their primary substrate.
Article
Biochemistry & Molecular Biology
Sarah Henaut-Jacobs, Hemanoel Passarelli-Araujo, Thiago M. Venancio
Summary: In this study, a network-based analysis of all publicly available Campylobacter genomes was conducted to explore the structure and diversity of the genus, revealing potential new species and elucidating genus features. The researchers also proposed a new species hypothesis and found a negative correlation between pangenome fluidity and saturation coefficient in different Campylobacter species, which could help estimate pangenome metrics of less sequenced genomes and understand their lifestyle and niche adaptation.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Review
Infectious Diseases
Langgeng Agung Waskito, Yudith Annisa Ayu Rezkitha, Ratha-korn Vilaichone, I. Dewa Nyoman Wibawa, Syifa Mustika, Titong Sugihartono, Muhammad Miftahussurur
Summary: Bacterial resistance to antibiotics has significant impacts on healthcare, government, and the economy. Culture-based methods for identifying resistant bacteria have limitations, and new approaches such as metagenomics and metatranscriptomics offer advantages in overcoming these limitations and improving diagnostic and management capabilities for resistant infectious diseases.
Article
Biochemical Research Methods
Joshua D. Harling-Lee, Jamie Gorzynski, Gonzalo Yebra, Tim Angus, J. Ross Fitzgerald, Tom C. Freeman
Summary: This study presents the use of an open-source network analysis platform, Graphia, to generate and analyze interactive 3D network graphs for studying the structure of bacterial populations, gene distribution, and syntenic order. The scalability to large genome datasets makes it valuable for the microbial research community.
BMC BIOINFORMATICS
(2022)
Article
Food Science & Technology
Mingyu Li, Mingyue Shen, Jingnan Lu, Jun Yang, Yousheng Huang, Lei Liu, Heyu Fan, Jianhua Xie, Mingyong Xie
Summary: This review summarizes the formation of harmful Maillard reaction products in dairy products during thermal processing, focusing on the occurrence, analysis methods, and inhibition of AGEs formation. It highlights the importance of monitoring and controlling the quality of dairy products.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Sina Beier, Nicholas R. Thomson
Summary: Panakeia is an easy-to-use tool that provides a detailed view of the pangenome structure, allowing for the discovery and in-depth analysis of features of interest. It analyzes the synteny and structural patterns of the pangenome, providing insights into the biological diversity and evolution of the studied taxon.
Article
Biology
Xin Huang, Zeyu Wang, Benzhe Su, Xinyu He, Bing Liu, Baolin Kang
Summary: The research proposed a computational strategy for metabolic network construction based on the overlapping ratio for studying the effect of disease treatment. Analysis of HD-pattern-dependent changes in plasma metabolites was conducted, revealing metabolic similarities and differences in patients' response to HD and HFD, providing guidance for personalized dialysis therapy.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Ana Belen Garcia-Martin, Thomas Roder, Sarah Schmitt, Friederike Zeeh, Remy Bruggmann, Vincent Perreten
Summary: This study provides insights into the genomic structure and variability of B. hyodysenteriae ST196, a predominant strain in Switzerland. The results reveal that Swiss B. hyodysenteriae isolates of the same ST may have evolved independently over time by point mutations and acquisition of larger genetic elements. The identification of a novel prophage, pphBhCH20, suggests that horizontal gene transfer events may drive changes in genomic structure.
Article
Biotechnology & Applied Microbiology
Jin-tian Li, Pu Jia, Xiao-juan Wang, Shi-wei Feng, Tao-tao Yang, Zhou Fang, Jun Liu, Bin Liao, Wen-sheng Shu, Jie-Liang Liang, Shu-ning Ou, Jing-li Lu
Summary: This study employed genome-centric metagenomics and metatranscriptomics to explore the diversity, metabolic potential, and gene expression profile of sulfate-reducing microorganisms (SRMs) in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. The study found that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. Additionally, viral genome sequences were found in both the metagenome and cultured model species, and these prophages encoded enzymes involved in glycoside hydrolysis and antioxidation. Furthermore, metatranscriptomic analysis revealed that the majority of SRMs in this environment were active, with an acidobacterial MAG containing a prophage dominating the SRM transcripts and expressing genes for its response to oxidative stress and competition for organic matter.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Review
Chemistry, Multidisciplinary
Efterpi Bouroutzika, Stavros Proikakis, Athanasios K. Anagnostopoulos, Angeliki Katsafadou, George C. Fthenakis, George Th Tsangaris
Summary: Cheese, a globally produced and consumed commodity, comes in various types with different production methods, with some countries labeling their most traditional cheeses as PDO. Studies show that proteomics can be used to enhance cheese labeling and production methods.
APPLIED SCIENCES-BASEL
(2021)
Review
Food Science & Technology
Aili Li, Xueting Han, Libo Liu, Guofang Zhang, Peng Du, Chao Zhang, Chun Li, Bingcan Chen
Summary: Obesity is a global public health problem that affects people's quality of life. Dairy products, which contain essential nutrients such as proteins, lipids, vitamins, and minerals, have been found to be effective in weight loss interventions for overweight/obese populations. This paper focuses on the relationship between the consumption of different dairy products and obesity, as well as the mechanisms by which functional components in dairy products regulate glucose and lipid metabolism and interact with gut microbes. It also discusses the role of dairy products in childhood and adolescent obesity.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Food Science & Technology
Simon Begrem, Marc Jerome, Francoise Leroi, Christine Delbarre-Ladrat, Olivier Grovel, Delphine Passerini
Summary: This study classified 47 Serratia isolates from seafood based on a phylogeny of the luxS gene, identifying S. proteamaculans as the main species in seafood products. Pangenome analyses of S. proteamaculans and S. liquefaciens showed high adaptation potential, revealing their involvement in biosynthetic pathways of antimicrobial compounds and seafood spoilage compounds. The genetic equipment highlighted in this study provided insights into the predominance of Serratia in seafood products and their spoilage capabilities.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2021)
Article
Microbiology
Hazem Ramadan, Maha Al-Ashmawy, Ahmed M. M. Soliman, Mohammed Elbediwi, Islam Sabeq, Mona Yousef, Abdelazeem M. M. Algammal, Lari M. M. Hiott, Mark E. E. Berrang, Jonathan G. G. Frye, Charlene R. R. Jackson
Summary: Genome sequencing and analysis of five L. innocua isolates from milk and dairy products in Egypt revealed the presence of antimicrobial resistance gene fosX, 13 virulence genes, and a heat-resistant ATP-dependent protease gene clpL on a plasmid. This is the first report of L. innocua containing clpL-carrying plasmids, suggesting possible evolution of virulent L. innocua strains. Ongoing genomic research is important for identifying these potential genetic changes and developing preventive measures.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Marcos Paolinelli, Georgina Escoriaza, Cecilia Cesari, Sandra Garcia-Lampasona, Rufina Hernandez-Martinez
Summary: Grapevine trunk diseases, particularly hoja de malvon (HDM), pose a significant threat to wine and table grape production in Argentina and Uruguay. The study revealed differences in the microorganisms present in grapevine wood between symptomatic and asymptomatic plants affected by HDM, with a higher presence of certain fungi in plants with more severe symptoms.
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.