Article
Microbiology
Bin Wei, Gang-Ao Hu, Zhen-Yi Zhou, Wen-Chao Yu, Ao-Qi Du, Cai-Ling Yang, Yan-Lei Yu, Jian-Wei Chen, Hua-Wei Zhang, Qihao Wu, Qi Xuan, Xue-Wei Xu, Hong Wang
Summary: By analyzing the genomes of marine prokaryotes, it was found that at least 96.8% of their secondary metabolic potential remains unexplored. Metabolomics and genomics approaches of a marine-derived bacterium identified potential biosynthetic pathways of novel polyketides and known compounds. These findings provide valuable knowledge for targeted discovery and biosynthesis of novel marine prokaryotic natural products.
Article
Biotechnology & Applied Microbiology
Andres Cumsille, Nestor Serna-Cardona, Valentina Gonzalez, Fernanda Claverias, Agustina Undabarrena, Vania Molina, Francisco Salva-Serra, Edward R. B. Moore, Beatriz Camara
Summary: Exploring Brevibacterium strains from diverse ecosystems may lead to the discovery of new antibiotic-producing strains. The genome sequencing of Brevibacterium sp. H-BE7, isolated from marine sediments, revealed its potential to produce novel natural products. Pangenome analysis showed diverse biosynthetic gene clusters in different phylogenomic clades of Brevibacterium strains. Evaluating the antibacterial activity of strain H-BE7 identified the presence of bioactive compound 1-methoxyphenazine.
Article
Chemistry, Medicinal
Despoina Konstantinou, Rafael Popin, David P. Fewer, Kaarina Sivonen, Spyros Gkelis
Summary: Sponges form symbiotic relationships with diverse and abundant microbial communities, with cyanobacteria playing important roles. Genomic analysis of the cyanobacterial genus Leptothoe revealed sponge-associated strains showing features of symbiotic lifestyle despite genome reduction, harboring biosynthetic gene clusters for novel natural products. Comparisons with chemically rich cyanobacteria suggest Leptothoe as a promising candidate for biosynthesis of novel natural products in marine environments.
Article
Microbiology
Yoon-Hee Chung, Hiyoung Kim, Chang-Hun Ji, Hyun-Woo Je, Dongho Lee, Sang Hee Shim, Hwang-Soo Joo, Hahk-Soo Kang
Summary: The genus Streptomyces is a rich source of secondary metabolite biosynthetic gene clusters (BGCs), with many cryptic BGCs still undiscovered. Through comparative genomics, a specific phylogenetic lineage within Streptomyces with high and uncharacterized biosynthetic potential was identified. Members of this lineage carry numerous unique BGCs, making them a promising target for metabolite characterization studies.
Review
Chemistry, Medicinal
Linda Sukmarini
Summary: This article focuses on the recent discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs) from marine bacteria using genome mining and synthetic biology approaches. The biosynthetic studies are discussed, particularly the organization of targeted biosynthetic gene clusters associated with potential bioactivities of the encoded RiPPs.
Article
Biotechnology & Applied Microbiology
Alshaimaa M. Hamoda, Rania Hamdy, Bahgat Fayed, Mohamed Abouleish, Ashna Sulaiman, Mohamad Hamad, Sameh S. M. Soliman
Summary: Sponges serve as habitats for diverse microorganisms, with symbiotic bacteria like Bacillus spp. producing metabolites with significant antifungal activity against eukaryotic cells. These findings suggest a selective defensive role of these metabolites, particularly against fungi, which are major infectious agents to sponges.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ismail Marzuki, Ruzkiah Asaf, Mudian Paena, Admi Athirah, Khairun Nisaa, Rasheed Ahmad, Mudyawati Kamaruddin
Summary: The study suggests that utilizing a consortium of sponge symbiont bacteria is a feasible and promising approach for degrading PAHs. In experiments with anthracene and pyrene, the consortium was effective in degrading both compounds, with pyrene showing a lower degradation rate. The degradation products mainly consist of alcohols, aldehydes, carboxylic acids, and a small proportion of aromatic hydrocarbon components.
Article
Chemistry, Medicinal
Joao F. Almeida, Matilde Marques, Vanessa Oliveira, Conceicao Egas, Dalila Mil-Homens, Romeu Viana, Daniel F. R. Cleary, Yusheng M. M. Huang, Arsenio M. Fialho, Miguel C. C. Teixeira, Newton C. M. Gomes, Rodrigo Costa, Tina Keller-Costa
Summary: This study investigated marine microbiomes to identify bacteria with rich secondary metabolism and antimicrobial activities. Genomic analysis of 70 representative isolates led to the identification of 466 biosynthetic gene clusters and the discovery of antimicrobial activities against various pathogens. These findings provide valuable resources for studying antimicrobial activities and biosynthesis of marine bacteria.
Article
Biotechnology & Applied Microbiology
Ana Rodriguez Jimenez, Nadege Guiglielmoni, Lise Goetghebuer, Etienne Dechamps, Isabelle F. George, Jean-Francois Flot
Summary: This study provides insights into the genome of V. fluvialis, a lactic acid bacteria species. The species shows high intraspecific diversity and is distinct from other Vagococcus species. Sponge-isolated V. fluvialis strains carry a higher number of mobile genetic elements and are enriched in functions related to the marine environment.
Review
Multidisciplinary Sciences
Kirstin Scherlach, Christian Hertweck
Summary: Genetically encoded small molecules play key roles in ecological interactions and drug discovery, but are often difficult to detect due to low production and high rediscovery rates. Genome mining for biosynthetic gene clusters can help address these limitations, leading to the discovery of previously overlooked natural products.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Ismail Gumustop, Fatih Ortakci
Summary: Leuconostoc pseudomesenteroides is a lactic acid bacteria species with wide distribution in various ecological niches. Genomic characterization reveals low conservation of genes, indicating accessory genes as the driving force for genotypic distinction. The species forms distinct clades based on isolation source and shows evolutionary adaptation to different environments. It is also found to be a reservoir for the type IIA CRISPR-Cas system. These findings provide insights into the biotechnological potential of Ln. pseudomesenteroides in the dairy industry.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuan Yuan, Yaolei Zhang, Peijun Zhang, Chang Liu, Jiahao Wang, Haiyu Gao, A. Rus Hoelzel, Inge Seim, Meiqi Lv, Mingli Lin, Lijun Dong, Haoyang Gao, Zixin Yang, Francesco Caruso, Wenzhi Lin, Rute R. da Fonseca, Ding Wang, Xianyan Wang, Marianne H. Rasmussen, Mingming Liu, Jinsong Zheng, Liyuan Zhao, Paula F. Campos, Hui Kang, Maria Iversen, Yue Song, Xinyu Guo, Jiao Guo, Yating Qin, Shanshan Pan, Qiwu Xu, Lingfeng Meng, A. Yunga, Shanshan Liu, Simon Ming-Yuen Lee, Xin Liu, Xun Xu, Huanming Yang, Guangyi Fan, Kun Wang, Songhai Li
Summary: The study generated high-quality genome assemblies of 17 marine mammals, revealing unique and convergent genomic variations associated with the transition to aquatic life in marine mammal lineages. The research advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biotechnology & Applied Microbiology
Manigundan Kaari, Radhakrishnan Manikkam, Abirami Baskaran
Summary: Marine microbes have genetically evolved to survive different environmental stress factors by producing bioactive metabolites. These metabolites are generated by biosynthetic gene clusters (BGCs) in the microbial genome, which contain the necessary genes for enzyme production. Various tools and techniques have been developed to enhance microbial chemo diversity and activate these gene clusters, leading to the production of novel metabolites. Metagenomics and functional gene expression studies help in classifying and understanding the biosynthetic pathways of these metabolites. Bioinformatic tools are also effective in identifying and annotating BGCs in genomes.
MARINE BIOTECHNOLOGY
(2022)
Article
Microbiology
Samantha C. Waterworth, Shirley Parker-Nance, Jason C. Kwan, Rosemary A. Dorrington
Summary: The study reveals that marine sponges form symbiotic relationships with bacteria to perform specific functions within the host, with some bacterial taxa widely distributed among invertebrate hosts and exhibiting conserved functional potential at a family level.
Article
Chemistry, Multidisciplinary
Nguyet A. Nguyen, Zhenjian Lin, Ipsita Mohanty, Neha Garg, Eric W. Schmidt, Vinayak Agarwal
Summary: Marine sponges are a rich source of bioactive compounds produced by bacteria symbiotically associated with the sponge host. A gene cluster encoding a cryptic ribosomally synthesized and post-translationally modified peptide (RiPP) is conserved in sponge microbiomes across different oceans, indicating a unique conservation pattern compared to non-symbiotic bacteria. Enzymes responsible for halogenation and cyclodehydration reactions in RiPPs have been discovered in sponge microbiomes, showing diverse interactions with substrate peptides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Medicinal
Yihe Zhao, Agostinho Antunes
Summary: Within the Conidae family, species with different feeding habits originated in the Neogene period, with many developing a polyphagous nature in warm shallow waters. The multi-origin trait of these species demonstrates the potential of conopeptides in biomedical research. However, current research tends to prioritize fish-hunting Conus species, believing their peptides hold more promise in medical studies.
Article
Microbiology
Ricardo Barroso, Alexandre Vieira-Pires, Agostinho Antunes, Isabel Fidalgo-Carvalho
Summary: Translation: Cats and dogs are susceptible to SARS-CoV-2 infection in natural conditions, as shown by a seroepidemiologic survey conducted in Portugal. Antibodies against SARS-CoV-2 were detected in 21.74% of cats and 4.73% of dogs, indicating the potential role of domestic animals in the global transmission of SARS-CoV-2. Human-to-animal and cat-to-cat transmission may also contribute to the spread of the virus among these animals.
Review
Biotechnology & Applied Microbiology
Luana Ramos, Agostinho Antunes
Summary: Sexual reproduction is a diverse and widespread process influenced by environmental and genetic factors. Sex chromosomes play a crucial role in evolution, but sequencing these genomic elements presents challenges.
Article
Biochemistry & Molecular Biology
Jorge L. Ramirez, Jonas Lescroart, Henrique Figueiro, Juan Pablo Torres-Florez, Priscilla M. S. Villela, Luiz L. Coutinho, Patricia D. Freitas, Warren E. Johnson, Agostinho Antunes, Pedro M. Galetti, Eduardo Eizirik
Summary: Using whole genome sequences, this study investigates the ecological differentiation among five species from the genus Leopardus, and explores their genomic features, comparative demographic history and positive selection. The results show that divergent ecological strategies are reflected in genomic features, and that the demographic history of these cats is influenced by climate fluctuations and habitat specialization, resulting in distinct evolutionary trajectories. Additionally, a gene involved in vertebrate retinal neurogenesis was found to be under positive selection in a specific species with nocturnal and arboreal specializations, indicating its importance in adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Letter
Environmental Sciences
Siew Woh Choo, Ju Lian Chong, Philippe Gaubert, Alice Catherine Hughes, Stephen O'Brien, Anne-Lise Chaber, Agostinho Antunes, Sara Platto, Nick Ching-Min Sun, Li Yu, Klaus-Peter Koepfli, Tulshi Laxmi Suwal, Mukesh Thakur, Stephan Ntie, Elisa Panjang, Jayaraj Vijaya Kumaran, Tariq Mahmood, Sean P. Heighton, Dago Dorji, Bi Sery Gonedele, Bryan Raveen Nelson, Chabi A. M. S. Djagoun, Ing Hoe Loh, Prativa Kaspal, Siim Pauklin, Toby Michelena, Hongxiang Zhu, Leonard Lipovich, Xuechen Tian, Siwei Deng, Christopher E. Mason, Jingyang Hu, Robert White, Nicholas S. Jakubovics, Wei Yee Wee, Tze King Tan, Kum Thong Wong, Steve Paterson, Ming Chen, Yixin Zhang, Rofina Yasmin Othman, Larry C. Brown, Bairong Shen, Guanghou Shui, Mia Yang Ang, Yunqi Zhao, Yongming Li, Bo Zhang, Cheng Tung Chong, Yu Meng, Aloysius Wong, Jianzhong Su, Hasmahzaiti Omar, Hua Shen, Choo Hock Tan, Hongyu Xu, Ian C. Paterson, Minyan Wang, Chee-Kai Chan, Siyuan Zhang, Avirup Dutta, Tay Sun Tee, Noel P. D. Juvigny-Khenafou, Naresh V. R. Mutha, Muhamad Afiq Aziz
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Editorial Material
Ecology
Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, Jose A. Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklos Balint
Summary: Progress in genome sequencing has enabled the generation of large-scale reference genomes, representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, allowing comprehensive analyses in population and functional genomics, and are expected to revolutionize conservation genomics.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Infectious Diseases
Maylin Romero, Yovani Marrero-Ponce, Hortensia Rodriguez, Guillermin Aguero-Chapin, Agostinho Antunes, Longendri Aguilera-Mendoza, Felix Martinez-Rios
Summary: A novel method based on network science and similarity searching was developed to rapidly and accurately identify tumor-homing peptides (THPs). By leveraging Chemical Space Networks (CSNs) and applying centrality measures and multi-query similarity searching models, a set of promising THP leads were discovered.
Article
Environmental Sciences
Cristiana Moreira, Cidalia Gomes, Vitor Vasconcelos, Agostinho Antunes
Summary: Cyanobacteria interfere with water quality through cyanotoxin production and bloom formation. Faster, sensitive, and specific tools are needed for risk assessment. PCR coupled with DNA sequencing can detect cyanobacteria and their potential toxicity. Sampling on seven waterbodies in Portugal showed that ecosystems with blooms and heat waves had high potential of cyanotoxins, while absence of blooms and heat waves lowered the risk. Other ecological variables may interfere with cyanotoxin synthesis. Additional cyanotoxins should be included in monitoring programs.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Liliana Silva, Tito Mendes, Luana Ramos, Guojie Zhang, Agostinho Antunes
Summary: This study provides a comprehensive gene screening of olfactory receptors (ORs) in fish, leading to an updated universal nomenclature for fish ORs. The researchers hypothesize that the expansion of OR gene families sensitive to airborne molecules may be associated with the emergence of new breathing structures in early osteichthyans. Interestingly, the OR repertoire of modern actinopterygians did not increase as expected, indicating regulatory mechanisms compensating for gene load excess.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Editorial Material
Infectious Diseases
Guillermin Agueero-Chapin, Agostinho Antunes, Yovani Marrero-Ponce
Article
Infectious Diseases
Guillermin Agueero-Chapin, Agostinho Antunes, Jose R. Mora, Noel Perez, Ernesto Contreras-Torres, Jose R. Valdes-Martini, Felix Martinez-Rios, Cesar H. Zambrano, Yovani Marrero-Ponce
Summary: Microbial biofilms can cause various environmental and industrial issues, as well as impact human health. Despite their antibiotic resistance, there are currently no approved antibiofilm agents for clinical treatments. Antimicrobial peptides (AMPs), with their antibiofilm activity and ability to target multiple microbes, have motivated the development of new antibiofilm agents. However, the use of complex network approaches as assistant tools for this purpose has not been explored.
Review
Fisheries
Manuel J. Seixas, Rodrigo R. Domingues, Agostinho Antunes
Summary: Chondrichthyes, including sharks, rays, and chimaeras, are jawed cartilaginous fishes with major relevance to marine ecosystems and humanity. Facing threats and population declines, assessing molecular genetic variation in Chondrichthyans' transcriptomes provides valuable resources for genomics research. Transcriptomic data has revealed insights into evolution, physiology, morphology, and biomedical potential, with potential for further exploration and conservation.
Article
Biology
Ryan Rasoarahona, Pish Wattanadilokchatkun, Thitipong Panthum, Thanyapat Thong, Worapong Singchat, Syed Farhan Ahmad, Aingorn Chaiyes, Kyudong Han, Ekaphan Kraichak, Narongrit Muangmai, Akihiko Koga, Prateep Duengkae, Agostinho Antunes, Kornsorn Srikulnath
Summary: The research aims to enhance the ant colony optimization algorithm by integrating marker effectiveness indicators, providing cost-effective solutions for genetic assessments, breeding, and conservation efforts. The study addresses the trade-off between accuracy and cost, and provides valuable insights into real-world genetic studies.
Article
Fisheries
Thitipong Panthum, Pish Wattanadilokchatkun, Kitipong Jaisamut, Worapong Singchat, Syed Farhan Ahmad, Narongrit Muangmai, Prateep Duengkae, Agostinho Antunes, Kornsorn Srikulnath
Summary: In this study, the male-linked region of the jade perch was identified on chromosome 19, and a remnant of the amh gene was found in this region, which is considered a candidate gene for sex determination in teleosts.
Article
Biochemical Research Methods
Diogo Ribeiro, Rui Borges, Ana Paula Rocha, Agostinho Antunes
Summary: This study improved a statistical measure for assessing evolutionary signals, resulting in more accurate evaluations of phylogenetic associations. It also provided a more accessible and computationally efficient implementation of the measure.
