Article
Microbiology
Claudia Petrillo, Stefany Castaldi, Mariamichela Lanzilli, Matteo Selci, Angelina Cordone, Donato Giovannelli, Rachele Isticato
Summary: The study identified salt-tolerant microbes with plant fitness-enhancing activities as potential plant growth-promoting bacteria. Whole-genome analysis revealed gene clusters with plant growth-promoting and biocontrol functions, along with novel secondary-metabolite biosynthetic genes, indicating potential beneficial impacts on plant growth and protection. This suggests a promising alternative to the indiscriminate use of agrochemicals in modern agriculture.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
G. Gioia, M. Severgnini, P. Cremonesi, B. Castiglioni, J. Freeman, A. Sipka, C. Santisteban, M. Wieland, V. Alanis Gallardo, J. G. Scott, P. Moroni, M. F. Addis
Summary: Houseflies may serve as potential carriers of Mycoplasma spp., as they harbor strains that are genetically similar to those found in milk. These flies possess multiple pathogenicity genes. Understanding transmission routes is crucial for preventing and controlling the spread of this pathogen.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Pavel A. Andriyanov, Pavel A. Zhurilov, Daria D. Kashina, Anastasia Tutrina, Elena A. Liskova, Irina Razheva, Denis Kolbasov, Svetlana A. Ermolaeva
Summary: This study reports the first isolation of E. anophelis strain in Russia and its isolation from raw cow's milk. The strain displayed resistance to multiple antimicrobials and carried various antibiotic resistance determinants and virulence factors.
Article
Biotechnology & Applied Microbiology
Francielly Soares Oliveira, Rafaela da Silva Rodrigues, Antonio Fernandes de Carvalho, Luis Augusto Nero
Summary: This study genetically characterized Pediococcus pentosaceus ST65ACC obtained from Brazilian artisanal cheese, revealing its potential as a probiotic candidate with bacteriocinogenic properties, stress adaptation genes, and adhesion genes.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Microbiology
Joo Hyun Han, Sang Eun Lee, Sathiyaraj Srinivasan
Summary: Strain 18JY21-1(T) is a novel species of Paenibacillus, named Paenibacillus albiflavus sp. nov., based on phylogenetic, chemotaxonomic, and phenotypic data analysis.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ilias Apostolakos, Theodora Skarlatoudi, Kornilia Vatavali, Agathi Giannouli, Loulouda Bosnea, Marios Mataragas
Summary: Dairy products can pose challenges to food safety and quality due to diverse microorganisms. Lactic acid bacteria (LAB) are safe as food additives, while staphylococci contain toxin-related genes that contribute to pathogenic potential. LAB are rich in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Joanna Plawinska-Czarnak, Karolina Wodz, Magdalena Guzowska, Elzbieta Rosiak, Tomasz Nowak, Zuzanna Strzalkowska, Adam Kwiecinski, Piotr Kwiecinski, Krzysztof Anusz
Summary: In this study, Salmonella BO strain was isolated from human milk and analyzed using whole-genome sequencing, serosequencing, and genotyping. The results revealed that the strain belongs to Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M) and showed significant changes in gene sequences. The presence of antimicrobial resistance genes, although not directly implying antibiotic resistance phenotype, was also detected.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Food Science & Technology
Mohamed Ghamry, Li Li, Wei Zhao
Summary: The study evaluates the fermentation efficiency and intrinsic effects on bioactive substances produced by Lactobacillus apis, isolated from the bumblebee gut, and two different isolated Lactobacillus communities from breast milk and camel milk. The results show that treatments with L.BM and L.CM produce the highest levels of phenolics and flavonoids, with significant impact on antioxidant capacity.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Genetics & Heredity
Qingchun Wang, Haiying Bao, Zhijun Li
Summary: This study compares the genetic composition of Inonotus hispidus growing in Morus alba (MA) and Fraxinus mandshurica (FM). The results show that there are differences in the coding genes and total number of genes between MA and FM. This research provides a foundation for exploring the medicinal value of FM as MA from the perspective of genetic composition.
FRONTIERS IN GENETICS
(2023)
Article
Food Science & Technology
James A. Elegbeleye, Elna M. Buys
Summary: This study aimed to quantify and compare biofilm-induced proteolysis and lipolysis in Bacillus subtilis and Bacillus velezensis with planktonic cells. Differences were observed in cell counts and enzyme concentrations in biofilms and planktonic cells in UHT milk. The spoilage potential of biofilms and planktonic cultures was found to be strain-dependent with variations in proteolysis and lipolysis among different strains.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Ondrej Holy, Julio Parra-Flores, Sarah Lepuschitz, Maria Paula Alarcon-Lavin, Ariadnna Cruz-Cordova, Juan Xicohtencatl-Cortes, Jetsi Mancilla-Rojano, Werner Ruppitsch, Stephen Forsythe
Summary: This study investigated the putative virulence factors of six Cronobacter sakazakii strains isolated from powdered milk, identifying different sequence types and resistance genes. Some strains demonstrated high adherence and invasion abilities, while the cpa gene was not detected. Various virulence and resistance genes, as well as plasmids, were identified through whole-genome sequencing. Additionally, CRISPR matrices were observed in all strains, enhancing decision-making for health authorities to protect public health.
Article
Gastroenterology & Hepatology
Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Akira Uchida, Rikky W. Purbojati, Kavita K. Kushwaha, Alexander Putra, Puramadathil Sasi Santhi, Benjamin W. Y. Khoo, Anthony Wong, Vineeth Kodengil Vettath, Daniela I. Drautz-Moses, Ana Carolina M. Junqueira, Stephan C. Schuster
Summary: Bacillus cereus is commonly found in nature and can cause foodborne illnesses. Analysis of whole-genome sequences from two strains isolated from air showed a diarrheal potential, with resistance to ampicillin and fosfomycin but susceptibility to ciprofloxacin, tetracycline, and vancomycin.
Article
Biology
Hams M. A. Mohamed, Hanan H. Abd-Elhafeez, Omar A. Al-Jabr, Mona A. El-Zamkan
Summary: This study investigated the presence of A. baumannii, its antimicrobial resistance, and biofilm formation in raw milk samples from Qena, Egypt. The results showed a high detection rate of A. baumannii in the milk samples, with resistant isolates carrying various resistance genes. Additionally, the majority of A. baumannii isolates exhibited the ability to form biofilms.
Article
Microbiology
Daniela Mollova, Tonka Vasileva, Veselin Bivolarski, Ilia Iliev
Summary: Breast milk is important for newborns as it provides essential nutrients and beneficial bacteria. This study focuses on the enzymatic hydrolysis of oligosaccharides and prebiotics present in breast milk by the bacteria. The researchers isolated and identified lactobacillus fermentum as the main bacteria involved in this process, and found that breast milk oligosaccharides are potent inducers of bacterial enzyme secretion.
Article
Microbiology
Daniela Mollova, Mariyana Gozmanova, Elena Apostolova, Galina Yahubyan, Ilia Iliev, Vesselin Baev
Summary: Lactiplantibacillus plantarum is a diverse species of lactic acid bacteria found in various ecological niches. This study focused on the L. plantarum PU3 strain, which has potential as a probiotic agent. Genomic analysis revealed the strain's genetic determinants for various beneficial traits, while phenotypic analysis confirmed its tolerance to challenging environments. The absence of virulence factors and the presence of potential antimicrobial activity further highlight its promising potential for probiotic and therapeutic applications.
Article
Virology
Dann Turner, Andrey N. Shkoporov, Cedric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J. Rodney Brister, Nina Chanisvili, Rob A. Edwards, Francois Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtboke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Munoz, Janis Rumnieks, B. L. Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens
Summary: This article summarizes the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses from March 2021 to March 2022. It provides an overview of the new classifications proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. The taxonomy of bacterial viruses underwent significant changes, including the abolition of the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae, as well as the order Caudovirales, and the establishment of a binomial nomenclature system for species. Additionally, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
ARCHIVES OF VIROLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Rachel L. Evanowski, Sarah I. Murphy, Martin Wiedmann, Nicole H. Martin
Summary: Bacterial spores in raw milk can survive in harsh processing conditions encountered in dairy manufacturing. Low-spore raw milk is desirable to extend shelf life, expand distribution channels, and reduce spoilage. A previous study showed that on-farm intervention reduced spore levels, and it was found that a considerable proportion of consumers continue to consume fluid milk after the expiration date, highlighting the importance of reducing spore levels.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
N. H. Martin, R. L. Evanowski, M. Wiedmann
Summary: Raw milk can become contaminated with bacteria from environmental sources, the cow, and contaminated equipment. Understanding the presence of certain bacterial groups in raw milk is crucial for reducing their impact on processed dairy product quality. The total bacteria count is recommended as a microbiological indicator of raw milk quality and a whole-farm approach to raw milk quality is suggested to ensure continuous improvement in dairy product quality.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Food Science & Technology
C. Qian, S. Murphy, R. H. Orsi, M. Wiedmann
Summary: With advancements in AI technologies, the development and implementation of digital food systems are becoming more feasible. AI applications such as machine learning, natural language processing, and computer vision have the potential to enhance food safety in various ways. However, obstacles such as limited data sharing and collaborative research efforts hinder the commercial development of AI technologies in food safety. Future actions should focus on data privacy protection, data standardization, and the establishment of a collaborative ecosystem to drive innovations in AI applications for food safety.
ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Microbiology
Xingwen Wu, Hao Luo, Chongtao Ge, Feng Xu, Xiangyu Deng, Martin Wiedmann, Robert C. Baker, Abigail E. Stevenson, Guangtao Zhang, Silin Tang
Summary: In a previous study, multiplex-nanopore-sequencing based whole genome sequencing (WGS) accurately predicted the serotype of Salmonella within one day. However, a larger scale test was needed to evaluate the conclusions. In the current study, this method was evaluated with 69 Salmonella serotypes and the feasibility of using it for antimicrobial resistance gene (AMR) and virulence gene detection was explored. The study found that accurate in silico serotype prediction was achieved within about five hours of sequencing, and AMR and virulence gene detection had high precision. This study demonstrates the potential of multiplex-nanopore-sequencing based WGS for rapid Salmonella classification and AMR/virulence gene profiling in the food industry.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
T. T. Lott, M. Wiedmann, N. H. Martin
Summary: In the study, the bacterial outgrowth in milk pasteurized at different temperatures was evaluated. The results showed that storage temperature had a significant effect on bacterial concentrations, while high-temperature, short-time (HTST) pasteurization did not. The data indicated that storage temperature had a larger impact on the shelf life of fluid milk than HTST, and abuse temperatures allowed for the growth of certain bacteria species that cannot grow at lower temperatures.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Immunology
Ahmed Gaballa, Martin Wiedmann, Laura. M. M. Carroll
Summary: Phosphoethanolamine transferases (PET) are closely related to colistin resistance genes (mcr) and can confer resistance to the last-resort antimicrobial colistin. Through studying the sequence similarity and evolution patterns of mcr and PET, we identified 125 putative novel mcr-like genes that share similar evolutionary patterns with i-PET genes. Our findings suggest that PET genes can give rise to colistin resistance genes through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide PET genes to evolve to function in colistin resistance.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Madison C. C. Williams, Alexandra E. E. Reker, Shally R. R. Margolis, Jingqiu Liao, Martin Wiedmann, Enrique R. R. Rojas, Alexander J. J. Meeske
Summary: Type VI CRISPR systems use Cas13 to recognize viral mRNA, leading to cell dormancy. This study shows that when combined with DNA-cleaving restriction-modification (RM) systems, type VI CRISPR can help resuscitate cells from dormancy by cleaving the phage genome. The co-occurrence of Cas13 and RM systems enhances the neutralization of phage infections.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Anna Schumann, Alexa R. Cohn, Ahmed Gaballa, Martin Wiedmann
Summary: Antimicrobial resistance is a growing concern for human and animal health, and the last resort antibiotics like colistin are crucial. However, the methods for characterizing colistin resistance genes are limited. In this study, we found that commonly used E. coli B-strains are intrinsically resistant to colistin, leading to growth defects when transformed with mcr-expressing plasmids. This finding highlights the importance of selecting appropriate expression hosts for identifying and characterizing AMR genes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Claire N. Schamp, Nitin Dhowlaghar, Lauren K. Hudson, Daniel W. Bryan, Qixin Zhong, Elizabeth M. Fozo, Ahmed Gaballa, Martin Wiedmann, Thomas G. Denes
Summary: Bacteriophages can be evolved to have improved abilities to control specific foodborne pathogens. In this study, researchers selected for mutant phages with improved infection kinetics in whole milk through experimental evolution. They identified two gene mutations that affected the surface charge of proteins and demonstrated that the fat content in milk is crucial for the expression of this phenotype. The findings highlight the potential of experimental evolution in developing condition-specific phage-based biocontrols in the food industry.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biophysics
Astrid Gedas, Anna Draszanowska, Henk den Bakker, Francisco Diez-Gonzalez, Manuel Simoes, Magdalena A. Olszewska
Summary: This study aimed to assess the colonization ability of Listeria innocua (L.i.) on materials commonly found in food processing and packaging settings, as well as evaluate the effectiveness of four phytochemicals in controlling L.i. biofilms. Results showed that L.i. colonized silicone rubber and stainless steel surfaces most abundantly, while copper had the highest cell death rate. Surface hydrophobicity played a significant role in cell viability and biofilm formation, with copper being the least prone to attachment. Among the phytochemicals tested, trans-cinnamaldehyde exhibited the highest efficacy in reducing L.i. biofilms, particularly on PET and Si surfaces.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Agriculture, Dairy & Animal Science
S. Lau, M. Wiedmann, A. Adalja
Summary: With the increasing awareness of the economic and environmental impact of food waste, interventions have been proposed to reduce it. This study focuses on fluid milk and evaluates interventions to extend its shelf life. The findings suggest that increasing periodic equipment cleaning is the most cost-effective strategy for processing plants to improve fluid milk shelf-life, both economically and environmentally. The approaches presented here can help individual firms generate customized assessments for the shelf life of dairy products.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Estefania Novoa Rama, Matthew Bailey, Sanjay Kumar, Cortney Leone, Henk C. den Bakker, Harshavardhan Thippareddi, Manpreet Singh
Summary: Meat from broilers raised without the use of antibiotics is gaining popularity among consumers. This study aimed to investigate the dynamics of gut microbial populations in broilers raised under conventional and no antibiotics ever (NAE) practices. The results showed that the cecal microbiota of NAE broilers differed from that of conventional broilers, with the latter having a rich but less diverse microbiota. The ileal microbiota of NAE broilers was primarily populated by Lactobacillus, which exhibited a higher abundance compared to conventional broilers.
Article
Genetics & Heredity
Laura M. Carroll, Nicolo Piacenza, Rachel A. Cheng, Martin Wiedmann, Claudia Guldimann
Summary: A multidrug-resistant (MDR) DT104 complex lineage lacking artAB has been identified in the USA among humans and cattle. This lineage, known as the "U.S. artAB-negative major clade", lacks Gifsy-1 and gogB genes. The clade lost artAB, Gifsy-1, and gogB around 1985-1987. Further research is needed to understand the role of artAB, gogB, and Gifsy-1 in the virulence of DT104 in humans and animals.
MICROBIAL GENOMICS
(2023)
Article
Ecology
Jingqiu Liao, Xiaodong Guo, Shaoting Li, Sai Manohar Balu Anupoju, Rachel A. A. Cheng, Daniel L. Weller, Genevieve Sullivan, Hailong Zhang, Xiangyu Deng, Martin Wiedmann
Summary: Understanding the genomic variation of bacteria in different environments can provide valuable insights into the mechanisms underlying their adaptation and transmission. This knowledge is particularly important for pathogens and benefits public health surveillance. However, our understanding of bacterial genomic variation is limited due to a lack of studies in different ecological contexts. To overcome this limitation, we analyzed a large-scale genomic dataset of the bacterial genus Listeria, including the human pathogen L. monocytogenes, collected from natural and food-related environments in the United States. Our comparative genomics analysis revealed significant differences in genomic profiles between environments within each species. This variation is supported by environment-associated subclades and the presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. The core genomes of Listeria species are strongly associated with environments and can accurately predict the source of isolation in L. monocytogenes using machine learning. Our data suggest that Listeria populations have genetically adapted to different environments, potentially limiting their transmission from natural to food-related environments.
ISME COMMUNICATIONS
(2023)