Article
Genetics & Heredity
Ana C. Reis, Monica Cunha
Summary: The study conducted whole-genome comparative analyses of 70 strains of Mycobacterium bovis, revealing an open pangenome architecture with core and accessory genome components supporting diverse subpopulations. Functional annotation classified the genes into different categories, with polymorphisms in virulence-related genes impacting disease severity. This indicates a dynamic pangenome structure with high evolutionary potential and emphasizes the role of genetic variations in shaping virulence.
MICROBIAL GENOMICS
(2021)
Article
Biochemical Research Methods
Qihua Liang, Stefano Lonardi
Summary: PGV is a reference-agnostic representation of a species' pan-genome based on consensus ordering, enabling intuitive, effective, and interactive visualization of complex structural genomic variations. The PGV software can be easily installed via conda or downloaded from the website, with a companion browser available for testing using example bed tracks from the GitHub page.
BMC BIOINFORMATICS
(2021)
Article
Infectious Diseases
Qinming Cai, Yongcheng Huang, Li Zhou, Niya Hu, Yanling Liu, Fujia Guo, Qiong Liu, Xiaotian Huang, Yunyi Zhang, Lingbing Zeng
Summary: This study identified the virulence genes associated with Nocardia NC_YFY_NT001 and other Nocardia spp. through genomic analysis. It was found that NT001 can cause infected animal death and several virulence factors were identified for future studies. This study provided new insights for further research on Nocardia virulence mechanisms.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Multidisciplinary Sciences
Carlos F. Prada, Maria A. Casadiego, Caio C. M. Freire
Summary: This study performed a comparative analysis of Helicobacter species to investigate the variability and evolutionary origin of virulence factors (VF). The results identified microevolutionary events in urease and flagella genes during the evolution of this genus. The findings also revealed genetic differences between gastric Helicobacter species (GHS) and enterohepatic species (EHS) and their relationship with pathogenicity.
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
Biochemistry & Molecular Biology
Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
Summary: Advances in sequencing technology have enabled in-depth profiling of microbial communities through pan-genome and metagenome analysis. The combination of pan-genome and metagenome approaches is seen as a promising method for tracking microbial sources and deciphering population-level evolution. Advanced analytical techniques, including big-data based artificial intelligence, are expected to further enhance our understanding of microbial community patterns.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Immunology
Kumari Snehkant Lata, Swapnil Kumar, Vaibhav Vindal, Saumya Patel, Jayashankar Das
Summary: This study explores the pan-genome of Leptospira genus, revealing the functional features and interactions with human proteins. The phylogenetic analysis based on the pan-genome separates Leptospira into three major clades related to their pathogenicity. Furthermore, specific genes for pathogenic and saprophytic groups have been identified and functionally annotated. These findings provide new insights into the genomic features of Leptospira and are valuable for disease control.
MICROBIAL PATHOGENESIS
(2022)
Article
Microbiology
Kiran Kumari, Vaishnavi Rawat, Afreen Shadan, Parva Kumar Sharma, Sushanta Deb, Rajnish Prakash Singh
Summary: A metal-resistant bacterium, Pseudomonas parafulva OS-1, was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain showed growth under specific temperature, pH, and metal concentrations. Genomic analysis revealed unique features, such as β-lactam resistance and a type VI secretion system (T6SS), as well as genes related to stress protection and biomass degradation. Horizontal gene transfer (HGT) may have played a role in the complexity of the OS-1 genome. This study provides insights into metal stress resistance mechanisms and the potential biotechnological applications of P. parafulva OS-1.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Iago Rodrigues Blanco, Lucas Jose Luduverio Pizauro, Joao Victor dos Anjos Almeida, Carlos Miguel Nobrega Mendonca, Alessandro de Mello Varani, Ricardo Pinheiro de Souza Oliveira
Summary: This study compared the genomes of P. pentosaceus available in the public GenBank database, focusing on their pediocin-like bacteriocin repertoire. The analysis revealed a temporal signal in the pattern of gene gain and loss, indicating that the complete genetic repertoire of this bacterial group is still unknown. Thirteen bacteriocin genes from Class II and III were predicted, and four pediocin-like bacteriocins and their accompanying immunity genes were highlighted. In silico modeling showed differences in the helix motif compared to physically determined pediocin-like structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Microbiology
Yvonne O. Ogaji, Robert C. Lee, Tim I. Sawbridge, Benjamin G. Cocks, Hans D. Daetwyler, Sukhjiwan Kaur
Summary: This study used Oxford Nanopore long-read sequencing to generate high-quality genome and mitochondrial genome assemblies for 18 isolates of the Australian Ascochyta Blight (AB) complex, revealing differences and similarities between the pathogens. It was found that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic.
Article
Biochemistry & Molecular Biology
Lior Glick, Itay Mayrose
Summary: The study of intraspecific genomic variation in eukaryotic species has been a focus of recent genome resequencing projects, with the use of the pan-genome concept presenting advantages over reference-based methods. However, constructing pan-genomes for eukaryotic species remains a challenging task, requiring tailored analysis pipelines and hindering research reproducibility and comparison. The software package Panoramic aims to simplify pan-genome construction for eukaryotic species by providing a user-friendly interface and efficient data processing algorithms.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Qin Qiao, Patrick P. Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, Alan E. Yocca, Adrian E. Platts, Steven J. Knapp, Marc Van Montagu, Yves Van de Peer, Jiajun Lei, Ticao Zhang
Summary: Strawberry has become a model system for various research, with genomes of five different species sequenced in recent years. A study reported chromosome-scale reference genomes for five strawberry species, along with genome resequencing data for 128 additional accessions, providing valuable resources for future studies. The research also identified a new diploid species and explored the evolutionary dynamics of gene families, pointing out mutations associated with white pigmented fruit in different strawberry species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Carlos Caicedo-Montoya, Monserrat Manzo-Ruiz, Rigoberto Rios-Estepa
Summary: This study utilized 121 genome sequences of the genus Streptomyces to estimate genomic diversity and identify potential antibiotic gene clusters. The open pan-genome of Streptomyces was observed, with a high quantity of unique gene families across species. Phylogenetic relationships were described using multiple markers, and 33 biosynthetic gene clusters with antibiotic potential were identified.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Chaofang Zhong, Bingpeng Qu, Gang Hu, Kang Ning
Summary: This study revealed the pan-genome of 39 Campylobacter species, provided the most updated reconstruction of the global virulence gene pool of 39 Campylobacter species, and identified species-related virulence differences.
MICROBIOLOGY SPECTRUM
(2022)
Article
Infectious Diseases
Genglin Guo, Dechao Du, Yanfei Yu, Yuhang Zhang, Yunyun Qian, Wei Zhang
Summary: Streptococcus suis is an emerging zoonotic pathogen that causes severe infections in swine and humans, with serotype 2 being most frequently associated with infections. Understanding the genomic features of different virulent strains is important, with core genes involved in basic physiological functions and accessory genes related to evolution. Comparative analysis revealed significant differences in pilus clusters between virulent and avirulent strains, with avirulent strains having larger genomes and more prophage sequences.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Microbiology
Anniina Runtuvuori-Salmela, Heidi M. T. Kunttu, Elina Laanto, Gabriel M. F. Almeida, Kati Makela, Mathias Middelboe, Lotta-Riina Sundberg
Summary: Intensive aquaculture conditions expose fish to bacterial infections, leading to financial losses, antibiotic overuse, and the risk of antibiotic resistance. This study isolated and characterized F. columnare strains and phages against F. columnare from Finland and Sweden. The results showed that phages had modular infection patterns based on host genetic group. Despite differences, whole-genome sequencing of phages showed high genetic similarity to previously isolated F. columnare phages. These findings suggest the potential of phage therapy for controlling columnaris disease in aquaculture.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Valentina Laura Donati, Lone Madsen, Mathias Middelboe, Mikael Lenz Strube, Inger Dalsgaard
Summary: This study investigated the effects of antibiotics and phage therapies on the gut microbiota of rainbow trout fry, with a focus on the pathogen Flavobacterium psychrophilum. The results showed that both the infection and the administration of antibiotics caused dysbiosis in the fish gut. Additionally, the addition of phages altered the fish microbiota regardless of the presence of the target bacterium. However, there were no observed negative effects on fish health or growth. Further studies should focus on determining the benefits or disadvantages of these changes for fish health and the host immune response.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Sheng-Da Zhang, Laura Louise Lindqvist, Thomas Isbrandt, Ingrid Lykke Borre, Mario Wibowo, Maike Wennekers Nielsen, Ling Ding, Thomas Ostenfeld Larsen, Lone Gram
Summary: The biosynthetic genetic basis and pathway of solonamides in P. galatheae S2753 were revealed, which may lead to the industrial production of solonamides. The comparison between a solonamide-deficient mutant and wild-type S2753 demonstrated that solonamides stimulate the swimming behavior of S2753 and influence a few key physiological processes of the native producers. These compounds not only serve as novel drug candidates but also provide competitive benefits to the native producer for survival in nature.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yayu Wang, Xiaolin Wang, Shuai Sun, Canzhi Jin, Jianmu Su, Jinpu Wei, Xinyue Luo, Jiawen Wen, Tong Wei, Sunil Kumar Sahu, Hongfeng Zou, Hongyun Chen, Zhixin Mu, Gengyun Zhang, Xin Liu, Xun Xu, Lone Gram, Huanming Yang, Ertao Wang, Huan Liu
Summary: In this study, the associations between genotypic, phenotypic, and rhizoplane microbiota variables of foxtail millet are investigated. A total of 257 rhizoplane microbial biomarkers associated with key agronomic traits are identified. The composition of the rhizoplane microbiota is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Laura Louise Lindqvist, Scott A. Jarmusch, Eva C. Sonnenschein, Mikael Lenz Strube, Janie Kim, Maike Wennekers Nielsen, Paul J. Kempen, Erwin M. Schoof, Sheng-Da Zhang, Lone Gram
Summary: The antibiotic tropodithietic acid (TDA) produced by bacteria affects multiple phenotypes and plays a key role in coordinating the colonization process of the producer. TDA has diverse effects on motility, cell morphology, metal metabolism, and horizontal gene transfer systems. This study broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.
Article
Microbiology
Roberto Sanchez-Navarro, Matin Nuhamunada, Omkar S. Mohite, Kenneth Wasmund, Mads Albertsen, Lone Gram, Per H. Nielsen, Tilmann Weber, Caitlin M. Singleton
Summary: Microorganisms produce a wide variety of secondary metabolites, many of which are yet to be discovered. In this study, the authors assessed the genetic potential of microbes in wastewater treatment plants using genome mining and discovered numerous biosynthetic gene clusters, most of which likely encode novel compounds. The study also highlights the importance of long-read sequencing for assembling complete biosynthetic gene clusters.
Article
Microbiology
Jesper Juel Mauritzen, Emilie Sondberg, Panos G. G. Kalatzis, Line Roager, Lone Gram, Sine Lo Svenningsen, Mathias Middelboe
Summary: Bacterial populations communicate and coordinate behavior using quorum-sensing molecules. Vibrio anguillarum, a marine fish pathogen, has multiple quorum-sensing systems, but our understanding of its regulation is limited. This study identified the VanT-QS regulon and explored the diversity and trajectory of traits regulated by quorum sensing in V. anguillarum. Furthermore, it was found that quorum sensing controls various genes involved in essential processes and virulence properties, with significant strain-specific differences.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Panos G. Kalatzis, Jesper Juel Mauritzen, Caroline Sophie Winther-Have, Slawomir Michniewski, Andrew Millard, Maria Ioanna Tsertou, Pantelis Katharios, Mathias Middelboe
Summary: Bacteriophages are abundant in the oceans and play important roles in bacterial activity, diversity, and evolution. The non-tailed viruses (Class: Tectiliviricetes) are less studied compared to tailed viruses (Class: Caudoviricetes). This study reports the discovery of a new family of temperate phages, Asemoviridae, widely distributed in marine environments and found in Vibrio species. These phages interact with the host bacteria, potentially contributing to their global distribution through increased virulence and biofilm formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Jianmu Su, Yayu Wang, Mei Bai, Tianhua Peng, Huisi Li, Hui-Juan Xu, Guifang Guo, Haiyi Bai, Ning Rong, Sunil Kumar Sahu, Hanjun He, Xiangxiu Liang, Canzhi Jin, Wei Liu, Mikael Lenz Strube, Lone Gram, Yongtao Li, Ertao Wang, Huan Liu, Hong Wu
Summary: This study used a multi-omics approach to investigate the effects of environmental factors on the accumulation of monoterpenes in citrus peel. It was found that soil nutrients and root-associated microbiome play important roles in the production of monoterpenes. The soil environment, including high salinity and certain nutrients, can enhance monoterpene content in citrus peel by promoting the expression of specific genes. Additionally, interactions between rhizosphere microorganisms and the host immune system can activate terpene synthesis and contribute to monoterpene accumulation.
Article
Biotechnology & Applied Microbiology
Pernille Kjersgaard Bech, Sheng-Da Zhang, Nathalie Nina Suhr Eiris Henriksen, Mikkel Bentzon-Tilia, Mikael Lenz Strube, Lone Gram
Summary: Microbial secondary metabolites have significant impacts on biotic interactions within microbial communities, but their effects on assembly and development of these communities are not well understood. In this study, a model system was used to examine the influence of the marine biofilm-forming bacterium Phaeobacter inhibens, which can produce the antibiotic secondary metabolite tropodithietic acid (TDA), on the assembly of a natural seawater biofilm community. The results showed that the production of TDA strongly affected the composition and dynamics of the microbial community, indicating the potential importance of microbial secondary metabolites in shaping complex microbial communities.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Microbiology
Line Roager, Eva C. C. Sonnenschein, Lone Gram
Summary: Microalgae play a crucial role as primary producers in the ocean and have potential as sustainable producers of biotechnologically interesting compounds. The bacterial microbiomes associated with microalgae are important for their growth and health, and engineering these microbiomes can enhance the fitness of the algae. This study evaluated the impact of different DNA extraction protocols on DNA quantity and quality, as well as the composition of bacterial microbiomes associated with three microalgae species.
MICROBIOLOGY SPECTRUM
(2023)
Review
Biotechnology & Applied Microbiology
Marcus Petersson, Sandra W. Thrane, Lone Gram, Serge Muyldermans, Andreas H. Laustsen
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ariadni Droumpali, Yuyan Liu, Xavier Ferrer-Florensa, Claus Sternberg, Maria Dimaki, Aaron J. C. Andersen, Mikael L. Strube, Paul J. Kempen, Lone Gram, Rafael Taboryski
Summary: Although aquaculture plays a major role in food production, the use of antibiotics can contribute to antibiotic resistance. The use of probiotic bacteria, such as Phaeobacter inhibens, that produce tropodithietic acid (TDA) provides an alternative approach to disease control in aquaculture. This study investigates the biosynthesis of TDA by Phaeobacter inhibens on micro-structured polymeric surfaces, and highlights the potential of optimized surfaces for sustainable aquacultures.
Article
Microbiology
Daniel Castillo, Alexander Ravndal Hojsting, Andrea Roosvall, Giorgos Smyrlis, Johanna Jorgensen, Mathias Middelboe
Summary: This study successfully isolated and evolved F. psychrophilum phages using two simple and fast strategies. The evolved phages exhibited improved host range and infection efficiency, which could be used to expand the targeting range of phages and treat Flavobacterium infections.
PHAGE-THERAPY APPLICATIONS AND RESEARCH
(2022)
