Review
Biochemistry & Molecular Biology
Qingzhen Hou, Fabrizio Pucci, Fengming Pan, Fuzhong Xue, Marianne Rooman, Qiang Feng
Summary: This article reviews the application of metagenomic data in protein structure prediction and discovery. It introduces widely used metagenomic databases and analyzes how metagenomic data has contributed to the improvement of structure prediction methods. The article also discusses the role of metagenomes in the discovery of enzymes, new CRISPR-Cas systems, and antibiotic resistance genes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Genetics & Heredity
Km Sartaj, Alok Patel, Leonidas Matsakas, Ramasare Prasad
Summary: Renewable biofuels play a crucial role in long-term solutions to fossil fuel depletion, with plant biomass as a sustainable approach for their production. Metagenomics is a powerful tool for functional gene analysis and new enzyme discovery in the biofuel industry.
Article
Biology
Guilhem Sempere, Adrien Petel, Magsen Abbe, Pierre Lefeuvre, Philippe Roumagnac, Frederic Mahe, Gael Baurens, Denis Filloux
Summary: metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. It offers a flexible data model, supports incremental data feeding, allows for exhaustive content browsing, rapid narrowing to find specific records, and features various interactive data visualization tools.
Review
Microbiology
Rebecca C. Mueller, Jesse T. Peach, Dana J. Skorupa, Valerie Copie, Brian Bothner, Brent M. Peyton
Summary: Advances in sequencing technologies have expanded our knowledge of the diversity within the domain Archaea. Archaea found in thermoalkaline environments may have divergent communities and metabolic pathways compared to those in acidic or circumneutral systems. Emerging multi-omics approaches, such as proteomics and metabolomics, offer potential to enhance our understanding of archaea in extreme thermoalkaline systems.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Kaela K. Amundson, Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton, Michael J. Wilkins
Summary: The colonization and persistence of microorganisms in subsurface shales after hydraulic fracturing are influenced by resource utilization, resistance to viral predation, and physicochemical conditions. Understanding the diversity and dynamics of microbial communities in these engineered deep ecosystems is essential for management and treatment of microbial biomass in hydraulically fractured wells.
Article
Virology
Norsazilawati Saad, James W. Olmstead, Arvind Varsani, Jane E. Polston, Jeffrey B. Jones, Svetlana Y. Folimonova, Philip F. Harmon
Summary: This study describes viral diversity in wild and cultivated blueberries in Florida using a metagenomic approach, revealing a variety of plant virus species. Blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) were identified for the first time in Florida, along with a novel tepovirus (blueberry virus T) (BlVT). This is the first study to compare viral diversity in wild and cultivated blueberries using a metagenomic approach.
Article
Engineering, Environmental
Ruyin Liu, Zong Li, Ganghua Han, Shujuan Cun, Deyin Hou, Zhisheng Yu, Kai Xue, Xinchun Liu
Summary: The temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue were investigated. It was found that lytic phages were more active while temperate phages showed low activity. The study also revealed a strong correlation between sludge concentration and free virus and temperate phage communities, indicating a microbial density-dependent virus dynamics.
Article
Microbiology
Yun Fang, Jun Liu, Jian Yang, Geng Wu, Zhengshuang Hua, Hailiang Dong, Brian P. Hedlund, Brett J. Baker, Hongchen Jiang
Summary: The study investigated the composition and metabolic pathways of autotrophic microorganisms in lacustrine sediments along a salinity gradient using metagenomic analysis. The results showed that salinity had a significant impact on the abundance and community composition of autotrophs, as well as their carbon fixation and glycolysis pathways. The dominant lineage and carbon fixation pathway shifted with decreasing salinity. These findings provide insights into the physiological efficiency and metabolic versatility of autotrophic microorganisms in saline environments and their response to salinity.
Review
Biotechnology & Applied Microbiology
Yan Zhang, Jacob Nedergaard Pedersen, Bekir Engin Eser, Zheng Guo
Summary: The low biodegradability of synthetic plastics has led to serious plastic pollution. This review summarizes the recent advances and challenges in the biodegradation of polyethylene and polystyrene, and discusses various methods and tools for plastic degradation.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Agriculture, Multidisciplinary
Yu Xia, Wen Zhou, Yake Du, Yan Wang, Min Zhu, Yajiao Zhao, Zhengyun Wu, Wenxue Zhang
Summary: The saccharification power and liquefaction power of different types of daqu were found to vary, with microbial saccharifying enzymes from various microbes playing a role in the process. The study identified differential genes and highlighted the differences in microbial communities between daqu types, providing insights into the saccharification functional genes of daqu.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Microbiology
Jose F. Cobo-Diaz, Adrian Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencia-Ares, Paula Puente-Gomez, Eleni Likotrafiti, Paula Fernandez-Gomez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat Gonzalez-Raurich, Mercedes Lopez, Miguel Prieto, Paul Cotter, Avelino Alvarez-Ordonez
Summary: The study found that pig carcasses were a source of resistant bacteria that colonized the food processing environment, with drains and certain food-contact surfaces serving as reservoirs for the spread of antibiotic resistance genes (ARGs). Over time, there was an increase in abundance and diversity of ARGs, mainly assigned to Acinetobacter and associated with resistance to antimicrobials frequently used in the region. The presence of mobile genetic elements and lateral gene transfer events were mainly detected in drains at a later sampling time.
Article
Biotechnology & Applied Microbiology
James C. Kosmopoulos, Danielle E. Campbell, Rachel J. Whitaker, Elizabeth G. Wilbanks
Summary: Phages play important roles in microbial systems by lysing host cells, facilitating horizontal gene transfer, and coevolving with bacterial hosts. This study investigates phage-host interactions in the pink berry consortia and reveals the diversity of mechanisms bacteria use to resist phage infection. The study also highlights the potential evolutionary consequences of phage-host interactions in a natural microbial system.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Varada Khot, Marc Strous, Xiaoli Dong, Alyse K. Kiesser
Summary: This study investigates the resistance of an alkaliphilic consortium, largely composed of a cyanobacterium Candidatus Phormidium alkaliphilum, to viral predation. The results show that viral predation of the cyanobacteria in the consortium is low and does not affect the community dynamics. The study suggests that potential viruses and CRISPR-Cas-mediated immunity play an important role in the establishment and functional robustness of microbial communities.
MICROBIOLOGY SPECTRUM
(2023)
Review
Energy & Fuels
Danae Bregnard, Alessio Leins, Guillaume Cailleau, Andrea Vieth-Hillebrand, Florian Eichinger, Joy Ianotta, Richard Hoffmann, Joerg Uhde, Saskia Bindschedler, Simona Regenspurg, Pilar Junier
Summary: Extreme environments on Earth are home to diverse microbial life. These microorganisms are able to survive in extreme conditions, such as high temperature, pressure, pH, or salinity. The study of microbial diversity in deep geothermal reservoirs used for energy production is a relatively unexplored frontier. These reservoirs offer a unique opportunity to study life in the deep biosphere. Microbes in these environments can also have negative impacts on geothermal power plant systems. This review summarizes the current knowledge and uncertainties surrounding microbial life in deep geothermal reservoirs, and suggests that these reservoirs may host an unexpected microbial diversity.
Article
Microbiology
Daniel Muratore, Anthony D. Bertagnolli, Laura A. Bristow, Bo Thamdrup, Joshua S. Weitz, Frank J. Stewart
Summary: The genomes of marine microbes are influenced by nutrient cycles and ocean-scale gradients in nitrogen availability. This study investigated the effect of nutrient changes on genomic properties at smaller spatial scales, such as in oxygen minimum zones and detrital particles. The results showed that nitrogen availability shaped microbial and viral genome properties, with higher nitrogen content in particle-associated microbes and at depths with higher nitrogen availability. This discovery suggests that stoichiometry plays a role in microbial and viral evolution across different scales.
Article
Energy & Fuels
Alice Botturi, Federico Battista, Marco Andreolli, Filippo Faccenda, Salvatore Fusco, David Bolzonella, Silvia Lampis, Nicola Frison
Summary: This study investigated the production of PHA-rich microbial biomass as a novel feed additive in aquaculture using bio-based VFAs obtained from acidogenic fermentation of agricultural residues. The economic analysis showed potential for higher benefits compared to biogas production through anaerobic digestion.
Article
Biochemistry & Molecular Biology
Nicola Curci, Andrea Strazzulli, Roberta Iacono, Federica De Lise, Luisa Maurelli, Mauro Di Fenza, Beatrice Cobucci-Ponzano, Marco Moracci
Summary: Hemicellulases from hyperthermophilic archaea show promising potential as biocatalysts for the efficient hydrolysis of plant biomasses, particularly due to their stability in harsh conditions. Despite being less studied compared to bacterial counterparts, these enzymes demonstrate efficient monosaccharide release in the hydrolysis of xyloglucan oligosaccharides, indicating their valuable industrial applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ruifei Wang, Bettina Lorantfy, Salvatore Fusco, Lisbeth Olsson, Carl Johan Franzen
Summary: Cell mass and viability play a crucial role in the productivity of fermentation processes, especially in lignocellulosic media. Various methods were evaluated for quantifying yeast cell concentrations, with manual cell enumeration and colony forming unit enumeration proving to be the most reliable in lignocellulosic conditions.Developing reliable cell quantification methods in lignocellulosic contexts will further optimize and control fermentation processes.
SCIENTIFIC REPORTS
(2021)
Review
Engineering, Chemical
Luca Zuliani, Annabel Serpico, Mario De Simone, Nicola Frison, Salvatore Fusco
Summary: To address the global energy and environmental crisis, biofuels like bioethanol have gained attention. Lignocellulosic biomasses (LCBs) are recognized as important alternatives due to their sustainable, abundant, widespread, and cheap supply. However, challenges in cost-effective conversion into ethanol still exist, including energy-demanding pretreatments, expensive enzymes, and the need for fermenting microorganisms.
Article
Biochemistry & Molecular Biology
Houria Hamoudi, Simona Giacobbe, Andrea Strazzulli, Cinzia Pezzella, Giovanni Sannia, Marco Moracci, Alessandra Piscitelli, Mouloud Kecha
Summary: Novel laccase enzymes were discovered in Algeria with appealing catalytic properties, including two thermostable laccases purified and characterised from a newly isolated Streptomyces strain. The genome of the strain also contained genes for lignin-degrading enzymes, revealing metabolic potential for various applications.
PROCESS BIOCHEMISTRY
(2021)
Article
Chemistry, Medicinal
Andrea Bosso, Rosa Gaglione, Rocco Di Girolamo, Edwin J. A. Veldhuizen, Pilar Garcia-Vello, Salvatore Fusco, Valeria Cafaro, Maria Monticelli, Rosanna Culurciello, Eugenio Notomista, Angela Arciello, Elio Pizzo
Summary: In this study, the promising anti-biofilm and immunomodulatory activities of human HDP GVF27 against Burkholderia multivorans and Burkholderia cenocepacia were discovered. GVF27 exhibited inhibitory effects on the biofilms of both bacterial strains, and showed synergistic effects with ciprofloxacin. Furthermore, GVF27 demonstrated interaction with the lipopolysaccharides isolated from B. cenocepacia, and had the ability to mitigate the release of pro-inflammatory cytokines in human cells stimulated by the same endotoxin.
Article
Biochemistry & Molecular Biology
Roberta Iacono, Andrea Strazzulli, Rosa Giglio, Federica Bitetti, Beatrice Cobucci-Ponzano, Marco Moracci
Summary: The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. Discovery and use of robust biocatalysts to replace toxic chemical catalysts play a significant role in this transition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Virology
Martina Aulitto, Laura Martinez-Alvarez, Salvatore Fusco, Qunxin She, Simonetta Bartolucci, Xu Peng, Patrizia Contursi
Summary: This mini review provides a comprehensive summary of four decades of research on the SSV1 virus, which has played an important role in the archaeal kingdom and has been widely utilized in genomic, transcriptomic, and proteomic studies.
Article
Food Science & Technology
Nicola Ferremi Leali, Renato L. Binati, Francesco Martelli, Veronica Gatto, Giovanni Luzzini, Andrea Salini, Davide Slaghenaufi, Salvatore Fusco, Maurizio Ugliano, Sandra Torriani, Elisa Salvetti
Summary: This study provides insights into the metabolic signatures of strains in kombucha microbial community, facilitating the standardization of kombucha production and demonstrating the roles played by different strains in the fermentation process.
Review
Biochemistry & Molecular Biology
Federica De Lise, Roberta Iacono, Marco Moracci, Andrea Strazzulli, Beatrice Cobucci-Ponzano
Summary: Archaea is the third domain of life and has a closer relationship with eukaryotes than bacteria. They are valuable model systems for molecular biology and biotechnology. Methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are four groups of archaea with established genetic systems, making them suitable for studying archaeal genes' functions. Thermophiles are also used to investigate various aspects of archaeal biology and are a valuable source for biotechnological applications.
Review
Biochemistry & Molecular Biology
Roberta Iacono, Federica De Lise, Marco Moracci, Beatrice Cobucci-Ponzano, Andrea Strazzulli
Summary: Hyperthermophilic archaeal glycosidases are enzymes that break down complex sugars and polysaccharides at high temperatures. They have a unique structure that allows them to remain stable and functional in extreme environments. This review provides an overview of the current knowledge on the structures and functions of these enzymes and their potential applications in various fields, with a focus on their structural characteristics and catalytic activity.
ESSAYS IN BIOCHEMISTRY
(2023)