Article
Biotechnology & Applied Microbiology
Feng Guo, Joseph C. McAuliffe, Cristina Bongiorni, Jacob A. Latone, Mike J. Pepsin, Marina S. Chow, Raj S. Dhaliwal, Katherine M. Hoffmann, Bill T. Brazil, Meng H. Heng, Serina L. Robinson, Lawrence P. Wackett, Gregory M. Whited
Summary: In this study, a previously unknown cyanuric acid hydrolase enzyme, named CAH-PR, was discovered from public databases. The enzyme showed favorable enzymatic and physical properties, and high-yield expression in aerobic cell culture. Its kinetic parameters and modeled structure were similar to known cyanuric acid hydrolases, but the new enzyme exhibited surprising thermal and storage stability. The CAH-PR enzyme was applied to hydrolyze cyanuric acid to biuret in the presence of sodium sulfite, and then hypochlorite was used to inactivate the remaining enzyme and oxidize biuret to dinitrogen and carbon dioxide gases.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dan-dan Li, Jin-lan Wang, Ya Liu, Yue-zhong Li, Zheng Zhang
Summary: Glycoside hydrolases (GHs) have multiple evolutionary origins and are structurally derived from 27 homologous superfamilies and 16 folds, with a bias towards a few superfamilies and folds. Different superfamilies exhibit variations in enzyme function, with some showing extreme functional diversity that is highly correlated with sequence diversity. Convergent evolution is observed in over one-third of glycosidase activities, especially in the degradation functions of GHs on polysaccharides.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Engineering, Environmental
Qianjie Xie, Wenfang Si, Zheng Wang, Yu Shu, Cong Li, Yehua Shen, Hiroshi Uyama
Summary: This study successfully controlled the sp3 defect density in metal-free carbon catalysts by constructing a core-shell structure with a rigid shell on the surface of polymeric precursor microspheres. The sp3 defects were effectively controlled by varying the thickness of the shell. Increasing the sp3 defect density significantly enhanced the oxygen reduction reaction (ORR) activity of the carbon catalysts. Theoretical calculations revealed that synergizing with graphitic-N can enhance the intrinsic ORR activity of sp3 defects. Therefore, the strategy of confined space modulation is a promising approach for controlling the sp3 defect density in organics-derived carbon-based catalysts.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Pavol Bardy, Conor I. W. MacDonald, Roman Pantucek, Alfred A. Antson, Paul C. M. Fogg
Summary: A new type of membrane-containing bacteriophage called Jorvik has been identified and characterized, which infects freshwater bacteria and exhibits high virulence. This provides important experimental insights into phage diversity and interactions in microbial communities.
Review
Agriculture, Dairy & Animal Science
Mutamed M. Ayyash, Abdelmoneim K. Abdalla, Nadia S. AlKalbani, Mohd Affan Baig, Mark S. Turner, Shao-Quan Liu, Nagendra P. Shah
Summary: Selecting potential probiotic strains with physiological capacity to perform successfully in the gastrointestinal tract is crucial. Recent studies have focused on selecting and evaluating novel probiotic microorganisms, mainly bacteria, from various sources. Standardization of experimental conditions is needed for future probiotic assessment studies.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Food Science & Technology
Weikang Yang, Lingqia Su, Lei Wang, Jing Wu, Sheng Chen
Summary: This review focuses on starch-converting enzymes in the GH family, which have α(1-6) transglycosylation activity, and describes their structures, functions, and synthesis processes. The actions of these enzymes greatly increase the structure and function diversity of starch, and it remains potential to obtain more functional products through combining their catalytic activity or engineering these enzymes. Future research should aim to obtain more information about the biochemical properties, sequences, and 3D structures of these enzymes to deepen our understanding.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Masao Ohashi, Thomas B. Kakule, Man-Cheng Tang, Cooper S. Jamieson, Mengting Liu, Yi-Lei Zhao, Kendall N. Houk, Yi Tang
Summary: Hirsutellones are fungal natural products with a macrocyclic structure, and the biosynthetic pathway involves the cooperative action of several proteins, such as oxidoreductase and lipocalin-like protein, in oxidative cyclization and exo-specific cycloaddition processes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Yeying Zhang, Tiffany M. Pham, Chase Kayrouz, Kou-San Ju
Summary: Phosphonate natural products have been successfully used in medicine and biotechnology for their ability to inhibit essential cellular pathways. This study reports the complete biosynthetic pathway of argolaphos phosphonopeptides and uncovers the biochemical origins of aminomethylphosphonate (AMPn) and N-epsilon-hydroxyarginine, two important components of the antimicrobial function of argolaphos. The study also reveals the function of AglA, a heme-dependent monooxygenase, and provides insights into the potential functions of the YqcI/YcgG protein family. The findings contribute to our understanding of natural product biosynthesis and have implications for future drug discovery.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
On You Kim, Seung Yun Lee, Da Young Lee, Sun Jin Hur
Summary: This study developed simple methods for extracting chenodeoxycholic acid (CDCA) and synthesizing ursodeoxycholic acid (UDCA) from pig by-products. The enzymatic method using bile salt hydrolase (BSH) enzymes was found to be more efficient than the chemical method. The chemical method yielded UDCA amounts of 6.05 mg, 0.51 mg, 3.04 mg, and 1.26 mg per 100 g of the liver, stomach, small intestine, and large intestine, respectively. The amounts of UDCA synthesized per 100 g through the chemical and enzymatic methods for extracting CDCA were 3.48 g and 2.22 g, respectively. The procedure developed in this study was simplified by three stages compared to the conventional chemical method of extracting CDCA, and it also provided a technique for improving the utilization of pig by-products.
Article
Multidisciplinary Sciences
Ting Zhou, Kun Ning, Zhenghai Mo, Fan Zhang, Yanwei Zhou, Xinran Chong, Donglin Zhang, Yousry A. El-Kassaby, Jian Bian, Hong Chen
Summary: By assembling and analyzing the chloroplast genome of Ilex dabieshanensis, potential genetic markers for distinguishing different species within the Ilex genus were identified, along with divergent regions compared to other traditional Ilex tea species.
Article
Chemistry, Physical
Salila Pengthaisong, Beatriz Piniello, Gideon J. Davies, Carme Rovira, James R. Ketudat Cairns
Summary: This study reports the structure of TxGH116 enzyme and its catalytic mechanism. The results show that the catalytic acid/base interacts with the glycosidic bond in a perpendicular manner. This has important implications for the design of specific inhibitors.
Article
Biochemistry & Molecular Biology
Pavle Kravljanac, Edward A. Anderson
Summary: Triterpenoid natural products from the Schisandraceae family have posed a significant synthetic challenge. In this study, a novel synthetic strategy was proposed to efficiently synthesize the core ring system of these natural products. The strategy involved palladium-catalysed cascade cyclisation and demonstrated high efficiency in the formation of fused systems.
Article
Biochemistry & Molecular Biology
Majd Lahham, Shalinee Jha, Dominic Goj, Peter Macheroux, Silvia Wallner
Summary: The subfamily of sarcosine oxidase is a group of enzymes within the larger family of amine oxidases, widely distributed among different kingdoms of life. These enzymes have unique features such as substrate binding motifs and types of oxidation reactions, distinguishing them from other amine oxidase families.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Danielle A. A. Yee, Kanji Niwa, Bruno Perlatti, Mengbin Chen, Yuqing Li, Yi Tang
Summary: Genome mining revealed a conserved fungal biosynthetic pathway that lacked a core enzyme. Heterologous expression identified a highly modified cyclo-arginine-tyrosine dipeptide as the associated natural product. Biochemical characterization led to the discovery of a new arginine-containing cyclodipeptide synthase (RCDPS) that showed no sequence homology to known enzymes and is widely encoded in fungal genomes. Further research on the biosynthetic pathway led to the discovery of new compounds whose structures would not have been predicted without the knowledge of RCDPS function.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Thermodynamics
Quoc-Thai Pham, Wan-Chi Ni, Anh Ngoc Tram Mai, Chorng-Shyan Chern
Summary: The mechanisms and kinetics of non-isothermal polymerization of N,N'-bismaleimide-4,4'-diphenylmethane (BMI) with cyanuric acid (CA) were investigated, revealing that the free radical polymerization mechanism predominated in the BMI/CA reaction system. The study utilized various techniques such as DSC, H-1-NMR, ESR, and GPC to characterize the competitive free radical polymerization and aza-Michael addition reaction mechanisms involved.
THERMOCHIMICA ACTA
(2021)
Article
Gastroenterology & Hepatology
Levi Teigen, Prince P. Mathai, Michael Matson, Sharon Lopez, Daria Kozysa, Amanda J. Kabage, Matthew J. Hamilton, Byron P. Vaughn, Michael J. Sadowsky, Alexander Khoruts
Summary: The study identified Methanobrevibacter as the most abundant methane producer, with its relative abundance serving as a clear distinction between CH4+ and CH4- samples. A qPCR-based test on fecal samples can become a valuable tool in clinical assessment of CH4 producing status, with a detection threshold of 5.2 x 10(5) copies/g for mcrA gene.
DIGESTIVE DISEASES AND SCIENCES
(2021)
Article
Ecology
Prince P. Mathai, Jonathan H. Bertram, Soumesh K. Padhi, Vikash Singh, Isaiah E. Tolo, Alexander Primus, Sunil K. Mor, Nicholas B. D. Phelps, Michael J. Sadowsky
Summary: Elevated temperature was found to be the primary driver of zebra mussel mortality, with salinity also increasing the likelihood of death. Stress-induced mortality in zebra mussels was associated with significant increases in the relative abundance of putative opportunistic bacterial pathogens, particularly Aeromonas. Shotgun sequencing and qPCR analyses showed that pathogenic Aeromonas species were significantly more abundant in temperature-induced dead zebra mussels.
Article
Environmental Sciences
Reda A. Abou-Shanab, Cara M. Santelli, Michael J. Sadowsky
Summary: The study showed that certain soil bacteria can enhance the availability of arsenic in soil, thus increasing arsenic uptake by Pteris vittata plants. Specific bacterial strains significantly improved arsenic uptake by P. vittata, leading to higher bioconcentration factors and potential use in large-scale soil remediation.
INTERNATIONAL JOURNAL OF PHYTOREMEDIATION
(2022)
Article
Microbiology
Joaquin Rilling, Fumito Maruyama, Michael J. Sadowsky, Jacquelinne J. Acuna, Milko A. Jorquera
Summary: The use of CRISPR loci combined with PCR was found to be an effective method for specific tracking of Azospirillum strains in soil systems, as demonstrated by successful detection in substrates and wheat seedlings. This molecular tool can easily be adapted to other microbial inoculants carrying CRISPR loci and can complement other microbiological techniques.
Review
Biology
Paola Duran, Gonzalo Tortella, Michael J. Sadowsky, Sharon Viscardi, Patricio Javier Barra, Maria de la Luz Mora
Summary: This article emphasizes the potential of utilizing soil-suppressive microbiota as a natural source of biocontrol agents, proposing a strategy of plant-mediated selection of inoculants, and discussing the main effects of climate change on crops and pathogens.
Article
Geosciences, Multidisciplinary
Weibo Kong, Fuyuan Su, Qian Zhang, Satoshi Ishii, Michael J. Sadowsky, Samiran Banerjee, Mingan Shao, Liping Qiu, Xiaorong Wei
Summary: This study in the Loess Plateau of China reveals that soil erosion and deposition have significant impacts on bacterial communities and multifunctionality. Erosion reduces bacterial richness and multifunctionality, but deposition can alleviate these negative effects. The study suggests that sustainable soil management and restoration of degraded lands can benefit from understanding the interactions between erosion, deposition, bacterial communities, and soil multifunctionality.
Article
Environmental Sciences
Jeonghwan Jang, Valery E. Forbes, Michael J. Sadowsky
Summary: This study discovered the presence of Cutibacterium acnes strains in the gut microbiota of the marine polychaete Capitella teleta. These strains produce propionate and vitamin B-12, which are essential microbial metabolites for the host. C. acnes, as a member of the worm's core functional microbiota, is likely favored by the host gut environment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Environmental Sciences
Warish Ahmed, Stuart L. Simpson, Paul M. Bertsch, Kyle Bibby, Aaron Bivins, Linda L. Blackall, Silvia Bofill-Mas, Albert Bosch, Joao Brandao, Phil M. Choi, Mark Ciesielski, Erica Donner, Nishita D'Souza, Andreas H. Farnleitner, Daniel Gerrity, Raul Gonzalez, John F. Griffith, Pradip Gyawali, Charles N. Haas, Kerry A. Hamilton, Hapuarachchige Chandithal Hapuarachchi, Valerie J. Harwood, Rehnuma Haque, Greg Jackson, Stuart J. Khan, Wesaal Khan, Masaaki Kitajima, Asja Korajkic, Giuseppina La Rosa, Blythe A. Layton, Erin Lipp, Sandra L. McLellan, Brian McMinn, Gertjan Medema, Suzanne Metcalfe, Wim G. Meijer, Jochen F. Mueller, Heather Murphy, Coleen C. Naughton, Rachel T. Noble, Sudhi Payyappat, Susan Petterson, Tarja Pitkanen, Veronica B. Rajal, Brandon Reyneke, Fernando A. Roman, Joan B. Rose, Marta Rusinol, Michael J. Sadowsky, Laura Sala-Comorera, Yin Xiang Setoh, Samendra P. Sherchan, Kwanrawee Sirikanchana, Wendy Smith, Joshua A. Steele, Rosalie Subburg, Erin M. Symonds, Phong Thai, Kevin Thomas, Josh Tynan, Simon Toze, Janelle Thompson, Andy S. Whiteley, Judith Chui Ching Wong, Daisuke Sano, Stefan Wuertz, Irene Xagoraraki, Qian Zhang, Amity G. Zimmer-Faust, Orin C. Shanks
Summary: Monitoring pathogens like SARS-CoV-2 in wastewater using RT-PCR is effective for public health information, but there is a lack of standardized protocols for wastewater surveillance. Key strategies for improving accuracy include QA/QC measures, representative sampling, virus concentration, and clear data interpretation guidelines.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Joao Brandao, Chelsea Weiskerger, Elisabete Valerio, Tarja Pitkanen, Paivi Merilainen, Lindsay Avolio, Christopher D. Heaney, Michael J. Sadowsky
Summary: Beach sand and water are both important for human health and their microbiology has been studied for decades. The World Health Organization recently recommended including recreational beach sands in monitoring for enterococci and Fungi. Global climate change is affecting beach microbial contamination, and the changing world and human travel contribute to the spread of endemic allochthonous microbiota. In the future, alternative microbial standards will be necessary to ensure the health of beach users from both sand and water contaminants.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biodiversity Conservation
Qian Zhang, Macarena M. Araya, Marcia Astorga-Elo, Gabriela Velasquez, Joaquin I. Rilling, Marco Campos, Michael J. Sadowsky, Milko A. Jorquera, Jacquelinne J. Acuna
Summary: Plant microbiota associated with pioneer plants in the Central Volcanic Zone of Andes play a crucial role in their growth and adaptation to harsh conditions. This study analyzed the composition and potential functions of rhizobacteria in Parastrephia quadrangularis plants from three volcanoes in the Atacama Desert. The results showed that Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla. Each plant recruited specific rhizobacterial communities independently of the volcano slope. The predicted functions mainly involved chemoheterotrophy, nitrogen cycling, and symbiosis.
Article
Nutrition & Dietetics
Levi Teigen, Prince P. Mathai, Sharon Lopez, Michael Matson, Baila Elkin, Daria Kozysa, Amanda J. Kabage, Matthew Hamilton, Byron P. Vaughn, Michael J. Sadowsky, Alexander Khoruts
Summary: This study aimed to determine the effect of short-term plant- and animal-based eating patterns on ex vivo fecal H2S production in healthy human volunteers. The results showed that compared to animal-based diet, plant-based diet resulted in lower H2S production in most healthy individuals, although there were substantial individual variations. Taxonomic differences were observed between responders and non-responders, suggesting potential individualized H2S responsiveness to diet.
CLINICAL NUTRITION
(2022)
Article
Biodiversity Conservation
Weibo Kong, Xiaorong Wei, Yonghong Wu, Mingan Shao, Qian Zhang, Michael J. Sadowsky, Satoshi Ishii, Peter B. Reich, Gehong Wei, Shuo Jiao, Liping Qiu, Liling Liu
Summary: Afforestation can effectively rehabilitate degraded ecosystems, but it may deplete deep soil moisture, which in turn affects soil microbial community and functionality. This study found that afforestation significantly impacted soil bacterial community and functionality in a semi-arid region of China's Loess Plateau, particularly in the deep soil layers. Afforestation led to reduced bacterial diversity and functionality, increased sensitivity to changes in soil moisture, and decreased sustainability of the ecosystems. These negative impacts on deep soils are crucial for assessing the eco-environmental effects of afforestation and ensuring the sustainability of forest ecosystems in semi-arid and arid climates.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Environmental Sciences
Liping Qiu, Weibo Kong, Hansong Zhu, Qian Zhang, Samiran Banerjee, Satoshi Ishii, Michael J. Sadowsky, Jianlun Gao, Changzeng Feng, Jingjing Wang, Chunliang Chen, Tianhui Lu, Mingan Shao, Gehong Wei, Xiaorong Wei
Summary: This study investigated the diversity, composition, and co-occurrence networks of rhizosphere bacteria and fungi in six halophytes and bulk soils in a semiarid inland saline ecosystem. The results showed that the enhanced association between fungi and bacteria increased the complexity of microbial co-occurring networks in halophytic rhizosphere, contributing to higher microbial functions in this saline ecosystem.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Yuyin Zhou, Zheting Bi, Matthew J. Hamilton, Li Zhang, Rui Su, Michael J. Sadowsky, Sabita Roy, Alexander Khoruts, Chi Chen
Summary: This study investigated the metabolic changes induced by FMT in rCDI patients through metabolomic analysis of urine samples. The results showed that the concentration of p-cresol sulfate in urine rapidly increased, making it a potential therapeutic indicator for the effectiveness of antibiotics and FMT.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Microbiology
Hao Wang, Gary W. Feyereisen, Ping Wang, Carl Rosen, Michael J. Sadowsky, Satoshi Ishii
Summary: This study investigated the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of woodchip bioreactors (WBRs). The results showed that introducing denitrifying bacteria and adding acetate can enhance the nitrate removal efficiency of WBRs. Additionally, the study found that denitrifiers are unevenly distributed in WBRs.
MICROBIOLOGY SPECTRUM
(2023)