Article
Microbiology
Feifeng Zeng, Yonghong Zhu, Dongling Zhang, Zengqiang Zhao, Quansheng Li, Panpan Ma, Guoli Zhang, Yuan Wang, Shenjie Wu, Sandui Guo, Guoqing Sun
Summary: This study investigates the composition and distribution of halophilic and salt-tolerant microbial communities in the highly saline soil of Yuncheng Salt Lake. The research finds that the dominant species and abundance of salt-tolerant microorganisms change gradually with distance from the lake. These microorganisms exhibit mechanisms of salt tolerance by regulating the expression of specific genes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Cong-Cong Liu, Shan-Shan Dong, Jia-Bin Chen, Chen Wang, Pan Ning, Yan Guo, Tie-Lin Yang
Summary: In this study, a novel clustering algorithm called MetaDecoder was introduced, which can classify metagenomic contigs based on the frequencies of k-mers and coverages. Benchmark tests on simulated and real-world datasets demonstrated that MetaDecoder can effectively cluster metagenomic contigs and has the potential to be a promising approach.
Article
Biotechnology & Applied Microbiology
Jingjing Sun, Congyu Yao, Yujie Li, Wei Wang, Jianhua Hao, Yi Yu
Summary: In this study, a novel β-galactosidase was isolated from a deep-sea metagenome, overexpressed in Escherichia coli, and purified. The enzyme showed high activity at specific temperatures and pH conditions, and exhibited resistance to salt. Moreover, it displayed hydrolysis and transglycosylation activity towards substrates such as oNPG and lactose.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Masaomi Kurokawa, Koichi Higashi, Keisuke Yoshida, Tomohiko Sato, Shigenori Maruyama, Hiroshi Mori, Ken Kurokawa
Summary: The study reveals that the optimal growth temperature of microorganisms can be accurately predicted based on the fraction of seven amino acids in their genomic sequences. Building on this discovery, researchers developed a 'Metagenomic Thermometer' that can predict environmental temperatures using metagenomic data. The Metagenomic Thermometer was found to accurately predict temperature changes in different environments with minimal influence from other microorganisms.
Article
Biotechnology & Applied Microbiology
Rong Guo, Wei Zhang, Wei Shen, Guoliang Zhang, Taifeng Xie, Ling Li, Jiacuo Jinmei, Yiduan Liu, Fanyong Kong, Baozhu Guo, Benke Li, Yujiang Sun, Shuqin Liu
Summary: In this study, the gut microbiome of donkeys from six different regions was sequenced, revealing differences in composition and function of gut microbes among different geographic regions. This study is valuable for donkey gut microbiome research.
Article
Biotechnology & Applied Microbiology
Ping Li, Jiyang Jiang, Yifei Li, Yue Lan, Fan Yang, Jiao Wang, Yuxin Xie, Fei Xiong, Jinhui Wu, Hanmin Liu, Zhenxin Fan
Summary: The study observed significant differences in the gut microbiome of obese children compared to controls, with the bacterial pathogen Campylobacter rectus significantly more abundant in obese children. Functional annotation of microbial genes indicated the presence of gut inflammation in obese children, while the gut microbiomes of overweight children were in a transitional state between obese and control children. Additionally, Trichuris trichiura was found to be significantly more abundant in the guts of obese Mexican children compared to obese Chinese children, highlighting differences in gut microbial composition between populations.
Article
Biotechnology & Applied Microbiology
Jose Matias Irazoqui, Maria Florencia Eberhardt, Gonzalo Manuel Santiago, Ariel Fernando Amadio
Summary: Cheese whey is a valuable by-product of dairy industries, and can be used to produce whey protein concentrate. Enzymes can be used to further process this by-product and produce higher value products, such as whey protein hydrolysates. This study identified three novel enzymes from metagenomic DNA of dairy industry stabilization ponds, which showed activities comparable to commercial proteases. These enzymes could provide alternative methods for dairy industries to produce value-added products from industrial by-products.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew D. Millard, Willem van Schaik
Summary: In this study, ten state-of-the-art phage identification tools were compared and evaluated for their usage in microbiome research. VIBRANT and VirSorter2 achieved the highest F1 scores in the RefSeq artificial contigs dataset, while Kraken2 performed the best in the mock community benchmark. This study provides important metrics for assessing the performance of phage detection tools and discusses optimal strategies for their usage.
Article
Chemistry, Multidisciplinary
Christian Sonnendecker, Juliane Oeser, P. Konstantin Richter, Patrick Hille, Ziyue Zhao, Cornelius Fischer, Holger Lippold, Paula Blazquez-Sanchez, Felipe Engelberger, Cesar A. Ramirez-Sarmiento, Thorsten Oeser, Yuliia Lihanova, Ronny Frank, Heinz-Georg Jahnke, Susan Billig, Bernd Abel, Norbert Straeter, Joerg Matysik, Wolfgang Zimmermann
Summary: Enzyme-based hydrolysis is a promising strategy for sustainable recycling of plastics. A study found that the enzyme PHL7 can completely degrade plastics and the products can be used to synthesize new plastics.
Article
Food Science & Technology
Lijun You, Chengcong Yang, Hao Jin, Lai-Yu Kwok, Zhihong Sun, Heping Zhang
Summary: This study utilized deep metagenomic sequencing to analyze the microbiomes of various fermented milk products, revealing microbial diversity and unique characteristics. New species belonging to Lactobacillus, Streptococcus, Acetobacter, and Rothia genera were identified, indicating potential influences on food flavor and quality. The common presence of bacteriocins and bacteriophage sequences in these products was also highlighted, showcasing their importance in controlling undesirable microorganisms and uncovering complex interactions within microbial communities.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Jiayin Zhou, Xiaoli Yu, Jihua Liu, Wei Qin, Zhili He, David Stahl, Nianzhi Jiao, Jizhong Zhou, Qichao Tu
Summary: In this study, a curated functional gene database called VB(12)Path was developed for accurate metagenomic profiling of VB12 synthesis gene families in complex environments. The results revealed significant differences in VB12 synthesis processes between the ocean and the human intestine. This database is expected to be a valuable tool for studying cobalamin biosynthesis processes in both environmental and human microbiome research.
Article
Nutrition & Dietetics
Zhenyu Wang, Jingjing Li, Lingyan Ma, Xiangdong Liu, Hong Wei, Yingping Xiao, Shiyu Tao
Summary: Neonatal diarrhea is a severe disease in humans and pigs, but the role of gut virome has not been studied. Using metagenomic sequencing, the viral community of diarrheal and healthy neonatal piglets was characterized. The viral community of diarrheal piglets showed higher heterogeneity and elevated abundance of Myoviridae. Phages infecting Proteobacteria, especially E. coli, were dominant in neonatal diarrheal piglets. Genus E. coli- and genus listeria-infecting bacteriophages were identified as key biomarkers for discriminating between neonatal diarrheal piglets and healthy controls. These findings expand our understanding of the relationship among phages, bacteria, and diarrhea, and may aid in the development of therapeutics for neonatal diarrhea prevention and treatment.
Article
Microbiology
Kenneth E. E. Schackart III, Jessica B. Graham, Alise J. Ponsero, Bonnie L. Hurwitz
Summary: In this study, 19 metagenomic phage detection tools were evaluated, and 9 were systematically assessed. The results showed significant differences in the predicted phage communities among the different tools, with tools using a homology approach demonstrating lower false positive rates and robustness to eukaryotic contamination, while tools using a sequence composition approach showed higher sensitivity. The benchmark datasets developed in this study are publicly available for future comparability of new tools.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Qi Zhang, Nuohan Xu, Chaotang Lei, Bingfeng Chen, Tingzhang Wang, Yunting Ma, Tao Lu, Josep Penuelas, Michael Gillings, Yong-Guan Zhu, Zhengwei Fu, Haifeng Qian
Summary: The global crisis in antimicrobial resistance continues to grow, with human feces found to be broadly representative of the global resistome and potentially a hub for accumulating and disseminating resistance genes across different habitats.
Article
Engineering, Environmental
Mengyuan Ji, Ginevra Giangeri, Muhammad Usman, Chao Liu, Matteo Bosaro, Filippo Sessa, Paolo Canu, Laura Treu, Stefano Campanaro
Summary: This study explored a hybrid strategy using native microorganisms and magnetic biochar (MBC) to degrade plasticizers. The MBC treatment led to the degradation of diethyl phthalate (DP) and the production of various organic products. The study provides evidence of the potential cooperation between native biodegraders and MBC in removing phthalate plasticizers from soil and surface water.
CHEMICAL ENGINEERING JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Nisha Singh, Anshu S. Mathur, Ravi P. Gupta, Colin J. Barrow, Deepak K. Tuli, Munish Puri
Summary: Thermophilic anaerobic bacteria can produce a variety of lignocellulose degrading enzymes with unique structural features and different biomass degradation schemes. The focus of research is on exploring the opportunities and technological challenges of these enzyme systems in the biofuel industry.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Food Science & Technology
Yogita Lugani, Munish Puri, Balwinder Singh Sooch
Summary: Xylose reductase is an industrially important food enzyme that plays a crucial role in converting xylose into xylitol, with diverse applications in various industries.
EUROPEAN FOOD RESEARCH AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Reinu E. Abraham, Peng Su, Munish Puri, Colin L. Raston, Wei Zhang
Summary: The physicochemical properties of alginate, such as viscosity and molecular weight, were found to affect the release of encapsulated bioactives, showing differences in release efficiency and pattern at different stages.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biotechnology & Applied Microbiology
Munish Puri, Adarsha Gupta, Ross A. McKinnon, Reinu E. Abraham
Summary: Microalgae have the potential to be a valuable resource for biodiesel production, but the high energy costs associated with their cultivation, harvesting, and dewatering make algal biofuel production commercially unviable. As an alternative, microalgae biorefineries are being considered for producing bioactives to offset the costs of biofuel production. The authors suggest that producing algal bioactives through advanced manufacturing pathways, using a biorefinery approach, could be effective, profitable, and economical.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Agricultural Engineering
Nisha Singh, Reeta Rani Singhania, Poonam S. Nigam, Cheng-Di Dong, Anil Kumar Patel, Munish Puri
Summary: The bioprocessing of lignocellulosic biomass to produce bio-based products is gaining global attention under biorefinery setup. However, the commercial success at industrial scale is still inadequate due to irregular biomass supply chain, market uncertainties, and scale-up challenges. Global research efforts by public and private sectors are underway to achieve deeper market penetration for the commercial success of lignocellulosic biorefineries.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Medicinal
Thi Nhu Thuong Nguyen, Timothy Chataway, Ricardo Araujo, Munish Puri, Christopher Milton Mathew Franco
Summary: In this study, a novel alginate lyase, AlyDS44, was purified and characterized from a marine actinobacterium, Streptomyces luridiscabiei, isolated from decomposing seaweed. AlyDS44 is a bifunctional alginate lyase active on both polyguluronate and polymannuronate, with a preference for degrading polyguluronate. It has optimal activity at pH 8.5 and 45°C, and shows salt tolerance with optimal activity at 0.6 M NaCl. Metal ions Mn2+, Co2+, and Fe2+ increased its activity, while Zn2+ and Cu2+ inhibited it. The enzyme belongs to the polysaccharide lyase family 7 and mainly produces disaccharides, trisaccharides, and tetrasaccharides when degrading alginate, functioning as an endo-type alginate lyase with potential for efficient production of alginate oligosaccharides.
Review
Biotechnology & Applied Microbiology
Adarsha Gupta, Colin J. Barrow, Munish Puri
Summary: Marine oleaginous protists, known as thraustochytrids, have the potential to produce various bioactive compounds. Developing a biorefinery could help offset production costs and enable large-scale, cost-competitive production.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Adarsha Gupta, Max J. H. Worthington, Harshal D. Patel, Martin R. Johnston, Munish Puri, Justin M. Chalker
Summary: A novel strategy for enriching saturated triglycerides produced in thraustochytrids is reported in this study. The method involves the direct reaction of elemental sulfur with the algae oil extract, leading to copolymerization of sulfur with unsaturated triglycerides and providing a new route to multiple useful materials. The unreacted oil can be separated for potential use in biodiesel production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Chemistry, Medicinal
Adarsha Gupta, Max J. H. Worthington, Justin M. Chalker, Munish Puri
Summary: This study demonstrates a bioprocessing approach using low-molecular-weight compounds to manipulate the fatty acid profile in a thraustochytrid strain to produce desirable fatty acids. Interestingly, the addition of D-limonene repressed the production of polyunsaturated fatty acids. This work has industrial value and suggests the use of sulfur polymerization for the preparation of plant-like oils using tuneable thraustochytrid lipids.
Article
Green & Sustainable Science & Technology
Samuel Rollin, Adarsha Gupta, Munish Puri
Summary: Enzymatic disruption of thraustochytrid cells using crude pineapple filtrate is an effective and non-toxic method to enhance lipid recovery.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Microbiology
Kritee Mehdiratta, Sonam Nain, Meenakshi Sharma, Shubham Singh, Sonali Srivastava, Bhushan Dilip Dhamale, Debasisa Mohanty, Siddhesh S. S. Kamat, Vivek T. T. Natarajan, Rakesh Sharma, Rajesh S. S. Gokhale
Summary: Our studies with freshwater Streptomyces sp. strain MNU77 demonstrate the conditional transcriptional upregulation and metabolic abundance of Polyketide quinones (PkQs) in the spore state of the Streptomyces life cycle. In addition, the downregulation of menaquinones, the only known electron carrier in Streptomyces, suggests the utilization of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.
MICROBIOLOGY SPECTRUM
(2023)
Article
Green & Sustainable Science & Technology
Priyanshu Jain, Shovon Mandal, Amritpreet Kaur Minhas, Munish Puri, Colin J. Barrow
Summary: Burning agricultural waste leads to local air pollution and global warming. A study aims to develop efficient nano-silica-based biocatalysts for concentrating omega-3 fatty acids in algal oil. The immobilized nano-systems created using physical adsorption approach showed the highest enzyme activity and binding efficiency.
JOURNAL OF CLEANER PRODUCTION
(2023)
Editorial Material
Biochemistry & Molecular Biology
Munish Puri, Adarsha Gupta, Shweta Sahni
TRENDS IN MICROBIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Samuel Rollin, Adarsha Gupta, Christopher M. M. Franco, Surinder Singh, Munish Puri
Summary: This study examines the techniques and importance of sustainable alternatives for the extraction and processing of nutritional oils. The findings suggest that adopting environmentally friendly alternatives can improve efficiency and reduce toxicity, thereby meeting global needs more effectively.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Priyanshu Jain, Amritpreet Kaur Minhas, Sadhana Shukla, Munish Puri, Colin J. Barrow, Shovon Mandal
Summary: This study isolated several indigenous microalgal strains from the Arabian Sea coast and identified two strains with high production of polyunsaturated fatty acids (PUFAs). The strains showed higher PUFA content, particularly alpha-linolenic acid, under low nutrient conditions.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
