Article
Biochemistry & Molecular Biology
Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvonen, Florian Hollfelder
Summary: The abundance of protein sequence data is not matched by the number of experimentally verified functional annotations. In this study, we used high-throughput microfluidic droplet screening to identify a new beta-glucuronidase enzyme with little homology to previously studied enzymes. This finding demonstrates the potential of functional metagenomics in uncovering the function of enzymes that cannot be predicted by bioinformatics.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Betulia de Morais Souto, Ana Carolina Bitencourt de Araujo, Pedro Ricardo Vieira Hamann, Andressa de Rezende Bastos, Isabel de Souza Cunha, Julianna Peixoto, Ricardo Henrique Kruger, Eliane Ferreira Noronha, Betania Ferraz Quirino
Summary: Functional screening of a metagenomic library from a Caatinga biome goat rumen led to the identification of a novel GH3 enzyme, BGL11, with multifunctional activities towards xylose-based substrates. This enzyme, BGL11, shows potential for industrial applications in plant biomass deconstruction for biofuel production.
Article
Ecology
Xiyang Dong, Haoyu Lan, Liangtian Huang, Haikun Zhang, Xianbiao Lin, Shengze Weng, Yongyi Peng, Jia Lin, Jiang-hai Wang, Juan Peng, Ying Yang
Summary: This study assessed the microbial communities in surface sediments from 16 coral reef sites at different depths in the Xisha islands using gene- and genome-centric metagenomics. The results revealed the diversity and functional potential of the microbial communities, as well as the presence of antibiotic resistance genes. These findings contribute to a better understanding of the microbial ecology in reef sediments.
Article
Agronomy
Temitayo Tosin Alawiye, Olubukola Oluranti Babalola
Summary: Microbial communities in the sunflower rhizosphere play a crucial role in plant growth and share similarities with bulk soil microbiomes. The rhizosphere harbors beneficial genes like nitrogen fixation and phosphate-solubilizing genes, aiding plants in adapting to environmental stresses. The presence of potential functional genes in the rhizosphere suggests their potential as biotechnological tools for sustainable agriculture, especially in light of the harm caused by indiscriminate pesticide use.
Article
Environmental Sciences
Bingkui Song, Zhihao Li, Si Li, Zhongzhen Zhang, Qitong Fu, Shijie Wang, Liang Li, Shuting Qi
Summary: Microorganisms can degrade petroleum hydrocarbons effectively with low cost and minimal side effects towards ecosystems. Metagenomic and metatranscriptomic analyses revealed the presence of diverse genes related to petroleum hydrocarbon metabolism and the synergistic transcription of genes in different pathways. The co-regulation of various metabolic pathways in exploiting nutrients derived from petroleum hydrocarbon metabolism is of great importance.
ENVIRONMENTAL POLLUTION
(2021)
Article
Microbiology
Xiaoqian Gu, Luying Zhao, Jiaojiao Tan, Qian Zhang, Liping Fu, Jiang Li
Summary: An agarase gene was obtained from macroalgae-associated bacteria collected from Antarctica and expressed in Escherichia coli. The recombinant enzyme exhibited optimal activity at 50 degrees C and pH 6.0, but was inhibited by Fe3+ and Cu2+. The enzyme primarily produced neoagarobiose, neoagarotetraose, and neoagarohexaose when degrading agarose substrate. The enzymatic hydrolysates, particularly dominated by neoagarobiose, significantly inhibited key pro-inflammatory markers.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Amani Alma'abadi, Hayedeh Behzad, Mohammed Alarawi, David Conchouso, Yoshimoto Saito, Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori
Summary: The demand for novel microbial biocatalysts in industrial and pharmaceutical applications is increasing rapidly. Advanced tools and technologies are needed to explore the metabolic potential of unculturable microorganisms. Single-cell and functional metagenomics studies have contributed to the discovery of unique microbial genes. In this study, a high-throughput single-cell microfluidic platform combined with fluorescent screening was used to discover new genes encoding lipolytic enzymes from the Red Sea.
Article
Food Science & Technology
Qiaozhi Song, Fangkun Zhao, Binbin Wang, Ye Han, Zhijiang Zhou
Summary: The traditional Chinese northeast suancai is a valuable food product, but its fermentation process can lead to the accumulation of nitrite, a common food safety issue. This study aimed to understand the biogeochemical cycle of nitrite and the microbial metabolic pathways involved in its degradation during suancai fermentation. The research identified key microbial species and enzymes responsible for nitrite reduction, providing insights for improving the safety of suancai through enzymatic degradation of nitrite.
FOOD RESEARCH INTERNATIONAL
(2021)
Article
Environmental Sciences
Zhenzhen Yan, Liping Ding, Dandan Zou, Jiarong Qiu, Yuting Shao, Shengwei Sun, Longxiang Li, Zhihong Xin
Summary: A novel carboxylesterase gene egyz5 was identified from a soil metagenomic library, and the recombinant enzyme EstYZ5 showed activity towards di(2-ethylhexyl) phthalate, which is rare for enzymes in the hormone-sensitive lipase (HSL) family. The high esterolytic activity and phthalate-degrading ability of EstYZ5 make it a promising candidate for biotechnological applications.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Chemistry, Medicinal
Patrick R. Fitzgerald, Wesley G. Cochrane, Brian M. Paegel
Summary: In this study, we demonstrated dose-response solid-phase DNA-encoded library screening method by modulating compound dose using UV intensity. The results showed dose-dependent hit rates for drug targets under different UV exposures. This method can prioritize hits for synthesis in drug lead identification.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Environmental Sciences
Ethan C. Cissell, Sophie J. McCoy
Summary: The proliferation of cyanobacteria in aquatic ecosystems worldwide due to anthropogenic factors is a growing concern. Despite extensive research on planktonic cyanobacterial blooms, benthic blooms of mat-forming cyanobacteria, especially on coral reefs, have not received enough attention. A study on the biodiversity of coral reef benthic cyanobacterial mat communities is essential for predicting and mitigating the impact of anthropogenic inputs on these ecosystems.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Microbiology
Ying Zhang, Chao Wang, Along Peng, Hao Zhang, Hongrong Wang
Summary: Thiamine supplementation has significant effects on carbohydrate-associated microorganisms and enzymes in the rumen of goats under subacute ruminal acidosis conditions, including increasing the abundance of fiber-related microorganisms and enzymes involved in fiber and starch degradation.
Article
Microbiology
Jie Li, Yiyang Zou, Jian Yang, Qiqi Li, David G. Bourne, Michael Sweet, Cong Liu, Anjie Guo, Si Zhang
Summary: Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. In this study, a total of 395 bacterial strains were isolated from the coral Pocillopora damicornis, with most of them representing potential novel species or genera. Genomic information derived from the isolates identified putative metabolic functions and various genes associated with establishing association with the coral host. This work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates.
Article
Chemistry, Medicinal
Yoshiko Okamura, Hirokazu Takahashi, Atsuyuki Shiida, Yuto Hirata, Haruko Takeyama, Katsuhiko Suzuki
Summary: Marine sponge-associated bacteria are known for producing bio-active compounds, and a metagenomic screening approach has been developed to identify novel genes and enzymes. Neutrophils play a crucial role in recognizing bacterial by-products which trigger the immune system response. The study focused on genes encoding amino acid ligase and peptide synthetase, with promising results in identifying molecules that engage the immune system against infection.
Article
Multidisciplinary Sciences
Philip J. A. Skipper, Lynda K. Skipper, Ronald A. Dixon
Summary: This study investigates the microbial biofilms on Lincolnshire limestone and identifies the core microbiome and differences between damaged and undamaged surfaces. The research provides significant new understanding in stone surface conservation and biodeterioration processes.
SCIENTIFIC REPORTS
(2022)
