Article
Biotechnology & Applied Microbiology
Brenda Rabello de Camargo, Andrei Stecca Steindorff, Leonardo Assis da Silva, Athos Silva de Oliveira, Pedro Ricardo Vieira Hamann, Eliane Ferreira Noronha
Summary: This study compared the gene expression profiling of Clostridium thermocellum B8 during growth on sugarcane bagasse and straw as carbon sources with growth on microcrystalline cellulose. The results showed that there were 625 and 509 up-regulated genes for growth on bagasse and straw, respectively. These genes were mainly involved in carbohydrate-active enzymes, cell motility, chemotaxis, quorum sensing pathway, and expression control of glycoside hydrolases. The findings highlight the impact of carbon source on the gene expression of carbohydrate-active enzymes and the importance of cell motility, attachment, and communication in degrading complex substrates. This research contributes to the development of enzymatic cocktails and industrial strains for biorefineries using sugarcane residues as feedstock.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Pedro R. Hamann, Luisa de M. B. Silva, Tainah C. Gomes, Eliane F. Noronha
Summary: The study demonstrated that utilizing mini-xylanosomes could enhance sugarcane deconstruction efficiency, while the mCipA protein could serve as a cellulose degradation enhancer.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Firnaaz Ahamed, Hyun-Seob Song, Yong Kuen Ho
Summary: The unified cybernetic-population balance model (UC-PBM) combines population balances and cybernetic models to simulate and understand the consolidated bioprocessing (CBP) of cellulose. It considers mechanisms of cellulose degradation and fermentative regulations for evaluating microbial potential and optimizing bioprocess design.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Ajaya K. Biswal, Neal N. Hengge, Ian M. Black, Melani A. Atmodjo, Sushree S. Mohanty, David Ryno, Michael E. Himmel, Parastoo Azadi, Yannick J. Bomble, Debra Mohnen
Summary: The study analyzed the solubilization of poplar biomass by Clostridium thermocellum during consolidated bioprocessing, showing a high solubilization rate of cellulose and non-cellulosic sugars with selectivity towards different sugars. However, the Rha-containing polymer in the solid residues was not effectively solubilized by C. thermocellum, indicating a potential barrier for efficient solubilization of poplar.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biotechnology & Applied Microbiology
Matthew R. Kubis, Evert K. Holwerda, Lee R. Lynd
Summary: Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum-mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum, which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2022)
Article
Microbiology
L. Podrzaj, J. Burtscher, K. J. Domig
Summary: This study presents draft genome sequences of 12 C. tyrobutyricum strains isolated from raw milk and cheese, which are recognized as the main causative agent of late blowing defect in hard and semihard cheeses.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Brigitte Cadieux, Opeyemi U. Lawal, Jean-Guillaume Emond-Rheault, Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Roger C. Levesque, John W. Austin, Lawrence Goodridge
Summary: Clostridium botulinum is a pathogen responsible for severe food-borne intoxication. This study reports the draft genome sequences of two C. botulinum strains and reveals the presence of multiple similar mobile genetic elements.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Jessica L. Halpin, Gerardo A. Gomez, Janet K. Dykes, Carolina Luquez
Summary: This study presents 20 draft genome sequences of Clostridium botulinum type A isolates from foodborne outbreaks in the United States and Ethiopia. These publicly available genomes enhance our understanding of C. botulinum genomics and are valuable for bioterrorism preparedness.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Lucia Fernandez, Ana Catarina Duarte, Beatriz Martinez, Ana Rodriguez, Pilar Garcia
Summary: This study compares the draft genome sequences of Staphylococcus aureus V329, a Bap-producing strain, and a derived mutant (BIM-1) resistant to phage phiIPLA-RODI, revealing a point mutation in the gene tagO in the mutant strain.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Oncology
Sulma Mohammed, Sagar Utturkar, Maxwell Lee, Howard H. Yang, Zhibin Cui, Nadia Atallah Lanman, GuangJun Zhang, Xavier E. Ramos Cardona, Suresh K. Mittal, Margaret A. Miller
Article
Biotechnology & Applied Microbiology
Kyle B. Sander, Daehwan Chung, Dawn M. Klingeman, Richard J. Giannone, Miguel Rodriguez, Jason Whitham, Robert L. Hettich, Brian H. Davison, Janet Westpheling, Steven D. Brown
BIOTECHNOLOGY FOR BIOFUELS
(2020)
Article
Cell Biology
Anna Pasechnek, Lev Rabinovich, Olga Stadnyuk, Gil Azulay, Jessica Mioduser, Tal Argov, Ilya Borovok, Nadejda Sigal, Anat A. Herskovits
Article
Oncology
Tram N. Dao, Sagar Utturkar, Nadia Atallah Lanman, Sandro Matosevic
Article
Microbiology
Inna Lysnyansky, Ilya Borovok
Summary: The study identified a prophage-like region in Mycoplasma bovirhinis HAZ141_2 with more than 40% GC content, including a highly transmittable gene cluster that confers high resistance to kanamycin and neomycin.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Microbiology
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goni Urriza, Dwayne A. Elias
Summary: ND132T strain, isolated from Chesapeake Bay, USA, is a sulfate-reducing and mercury-methylating bacterium with high levels of mercury methylation. It belongs to the genus Pseudodesulfovibrio and has been proposed as a new species, Pseudodesulfovibrio mercurii.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Plant Sciences
Nicholas C. Dove, Dawn M. Klingeman, Alyssa A. Carrell, Melissa A. Cregger, Christopher W. Schadt
Summary: The plant microbiome is crucial for plant health, but our understanding of it in regenerating plant communities is limited. Research shows that both soil and plant tissue microbiomes respond to fire. The impact of fire on plant microbiome assembly, diversity, and composition highlights the need for further study to enhance plant fitness and ecosystem recovery post-fire.
Article
Microbiology
Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan Lu, Leah H. Burdick, Sara S. Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa A. Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Summary: This study identified representative bacterial strains and established a culture collection of 3,211 isolates for exploring microbial function and community inoculation experiments. Through genome sequencing of representative strains, the study aims to further understand the functionality of microbial communities. Experimental results showed that a simplified microbial community of 10 members could effectively colonize Populus roots and interactions between microbes were studied.
Article
Microbiology
Dmitry A. Rodionov, Irina A. Rodionova, Vladimir A. Rodionov, Aleksandr A. Arzamasov, Ke Zhang, Gabriel M. Rubinstein, Tania N. N. Tanwee, Ryan G. Bing, James R. Crosby, Intawat Nookaew, Mirko Basen, Steven D. Brown, Charlotte M. Wilson, Dawn M. Klingeman, Farris L. Poole, Ying Zhang, Robert M. Kelly, Michael W. W. Adams
Summary: Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono-and oligosaccharides to produce ethanol and other industrially important end products. Transcriptional regulation mechanisms of carbohydrate utilization genes were investigated using a comparative genomics approach, revealing a complex regulatory network controlling the expression of genes involved in degradation of plant biomass. The reconstruction of carbohydrate utilization regulatory network improved functional annotations of transporters and catabolic enzymes, providing insights for metabolic engineering strategies to optimize yields of bio-based fuels and chemicals from lignocellulose, with a focus on Caldicellulosiruptor bescii.
Article
Microbiology
Etai Boichis, Nadejda Sigal, Ilya Borovok, Anat A. Herskovits
Summary: This study identified a conserved locus containing XRE regulators, a metzincin protease, and a lipoprotein structurally similar to a TIMP-family metzincin inhibitor, which play a crucial role in Listeria monocytogenes life cycle. The XRE regulators act as a regulatory switch that influences the expression of metzincin and TIMP-like genes, affecting Lm morphology and virion release. These proteins also modulate the cell wall structure and may hold promise in combating antibiotic resistant bacterial pathogens.
Article
Infectious Diseases
Inna Lysnyansky, Ilya Borovok
Summary: This study characterized recombination events and their consequences within the aadE*-sat4-aphA-3 containing region of the 54 kb GC-rich prophage region in Mycoplasma bovirhinis HAZ141_2. Recombination events including inversions via 155 and 197 bp repeats and the excision of the aadE*-sat4-aphA-3 cluster were confirmed, with effects on gene expression and antibiotic resistance profiles observed. The study highlights the genetic plasticity of the region and its impact on phenotype.
Correction
Plant Sciences
Alyssa A. Carrell, Melissa A. Cregger, Nicholas C. Dove, Dawn M. Klingeman, Christopher W. Schadt
Article
Biochemical Research Methods
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
Summary: Uncultivated Bacteria and Archaea, which make up the majority of Earth's species, can now have their genomes extracted using shotgun sequencing. The U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform offers a series of analysis steps and data products to facilitate the recovery of high-quality metagenome-assembled genomes (MAGs) from microbiomes. This platform allows users to go from sequencing reads to MAGs, which can be further analyzed with other KBase capabilities.
Correction
Biochemical Research Methods
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
Correction
Chemistry, Multidisciplinary
Lahiru N. Jayakody, Christopher W. Johnson, Jason M. Whitham, Richard J. Giannone, Brenna A. Black, Nicholas S. Cleveland, Dawn M. Klingeman, William E. Michener, Jessica L. Olstad, Derek R. Vardon, Robert C. Brown, Steven D. Brown, Robert L. Hettich, Adam M. Guss, Gregg T. Beckham
ENERGY & ENVIRONMENTAL SCIENCE
(2021)
