Article
Biotechnology & Applied Microbiology
Syed Usman Enam, Joshua L. Cherry, Susan R. Leonard, Ivan N. Zheludev, David J. Lipman, Andrew Z. Fire
Summary: A nuclease-based approach is developed to enrich DNA from specific organisms, improving the sensitivity of metagenomic sequencing. This method allows for rapid enrichment of pathogenic bacteria and can also be used to enrich for modified DNA that may go unnoticed in metagenomic samples.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Elizabeth G. Wilbanks, Hugo Dore, Meredith H. Ashby, Cheryl Heiner, Richard J. Roberts, Jonathan A. Eisen
Summary: The plasticity of bacterial and archaeal genomes makes it challenging to recover complete genomes from metagenomes. In this study, the researchers used strain-specific patterns of DNA methylation to successfully resolve complex bacterial genomes from metagenomic data. They recovered the largest and most complex circularized bacterial genome ever recovered from a metagenome and identified instances of horizontal gene transfer, phage infection, and strain-level structural variation.
Article
Biotechnology & Applied Microbiology
Mengge Wang, Guanglin He, Shuang Gao, Fuquan Jia, Xing Zou, Jing Liu, Shouyu Wang, Ziwei Ye, Yiping Hou, Zheng Wang
Summary: The study found that modern Mongolian populations have close genetic proximity to geographically northern East Asians, while also possessing relatively less Hainan Li-related ancestry and more northern East Asian-related ancestry.
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
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
Biochemistry & Molecular Biology
Mohamed M. Aboelnga, James W. Gauld
Summary: This study aims to evaluate the binding proficiency of potential inhibitors against threonyl-tRNA synthetases. Through quantum chemical study, binding energy value comparison, and molecular docking, several potent ligands have been suggested, which could be valuable in developing competitive inhibitors against bacterial ThrRS.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Yanhui Li, Neil Molyneaux, Haitao Zhang, Gang Zhou, Carly Kerr, Mark D. Adams, Kathleen L. Berkner, Kurt W. Runge
Summary: In this study, we developed an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes. By leveraging sequence information, we were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Lakshmi Narayanan, Ozan Ozdemir, Navatha Alugubelly, Reshma Ramachandran, Michelle Banes, Mark Lawrence, Hossam Abdelhamed
Summary: The study used Tn mutagenesis to identify genes and pathways affecting the growth and fitness of Listeria monocytogenes in minimal medium. The findings revealed that biosynthesis of purines, pyrimidines, ATP, and branched-chain fatty acids plays an important role in the pathogenesis of L. monocytogenes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Pavan Heggadadevanakote Kendaganna, Chandan Shivamallu, Govindaraju Shruthi, Mekhala Nagabushan Chitagudigi, Sushma Pradeep, Prashantha Karunakar, Amachawadi G. Raghavendra, Sharanagouda S. Patil, Asad Syed, Abdallah M. Elgorban, Ali H. Bahkali, Ravindra Veerapur, Shiva Prasad Kollur
Summary: Nosocomial infections, including those caused by Klebsiella pneumoniae, are highly virulent and often resistant to multiple drugs. The KPHS_00890 hypothetical protein of K. pneumoniae has been identified as a bifunctional 5'-nucleotidase, with a potential role in immune evasion strategies during infection.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2021)
Article
Parasitology
Binod Kumar, Biswa Ranjan Maharana, Bhupendrakumar Thakre, Nilima N. Brahmbhatt, Joice P. Joseph
Summary: The 18S rRNA PCR assay was standardized and optimized as a primary method for molecular screening of piroplasms in different animals, and it showed high sensitivity and specificity.
ACTA PARASITOLOGICA
(2022)
Article
Medicine, General & Internal
Astrid-Jane Williams, Ramesh Paramsothy, Nan Wu, Simon Ghaly, Steven Leach, Sudarshan Paramsothy, Crispin Corte, Claire O'Brien, Catherine Burke, Gabrielle Wark, Dorit Samocha-Bonet, Kelly Lambert, Golo Ahlenstiel, Valerie Wasinger, Shoma Dutt, Paul Pavli, Michael Grimm, Daniel Lemberg, Susan Connor, Rupert Leong, Georgina Hold
Summary: Crohn's disease and ulcerative colitis are common chronic inflammatory bowel diseases with unclear mechanisms. The Australian IBD Microbiota (AIM) Study aims to identify microbial signals and correlations to disease activity over time. By collecting extensive demographic, clinical, lifestyle and dietary data, the study seeks to understand the interaction between IBD patients and their microbiota.
Article
Fisheries
Lara Parata, Jesmond Sammut, Suhelen Egan
Summary: Freshwater fish farming is the largest sub-sector of the global aquaculture industry, with microbial research holding potential to further enhance the industry's success. However, existing literature on freshwater fish microbiology covers less than 1% of freshwater fish species, with a narrow focus on certain fish families and limited exploration of important areas such as fish fecundity and sustainability. Additional investments in microbial research are needed to ensure the continued expansion and success of freshwater aquaculture.
REVIEWS IN AQUACULTURE
(2021)
Article
Ecology
Jiasui Li, Marwan E. Majzoub, Ezequiel M. Marzinelli, Zhicong Dai, Torsten Thomas, Suhelen Egan
Summary: The study identified a specific bacterium, Phaeobacter sp. BS52, isolated from healthy Delisea pulchra, that showed antagonistic effects against bleaching pathogens and increased the proportion of healthy individuals. The protective action of BS52 was attributed to its ability to prevent dysbiosis rather than direct pathogen inhibition.
Article
Ecology
Jiasui Li, Florian Weinberger, Mahasweta Saha, Marwan E. Majzoub, Suhelen Egan
Summary: The development of marine probiotics has been limited, with a focus on farmed animals rather than seaweeds. This study demonstrates that non-endemic probiotics may be more effective in preventing diseases in certain seaweeds compared to endemic probiotics. The potential of utilizing probiotics that can function across different hosts to mitigate the impact of emerging marine diseases is highlighted.
Article
Biochemistry & Molecular Biology
Jadranka Nappi, Priscila Goncalves, Tahsin Khan, Marwan E. Majzoub, Anna Sophia Grobler, Ezequiel M. Marzinelli, Torsten Thomas, Suhelen Egan
Summary: Most multicellular eukaryotes host complex communities of microorganisms, and the settlement of specific microorganisms has a lasting impact on community composition, with different bacterial strains exhibiting idiosyncratic priority effects.
Article
Nursing
Catherine Burke, Yvonne Conway
Summary: This review aimed to identify and synthesize qualitative studies on factors influencing nurses' decision to escalate care in response to patients' Early Warning Score (EWS). Eighteen studies involving 235 nurses from seven countries were identified. The analysis identified four themes: marrying nurses' clinical judgement with EWS, SMART communication, the blessing and curse of EWS protocol, and the impact of the hospital domain.
JOURNAL OF CLINICAL NURSING
(2023)
Article
Biochemistry & Molecular Biology
Jennifer Hudson, Nandan Deshpande, Catherine Leblanc, Suhelen Egan
Summary: This study used mRNA-sequencing analysis to investigate the early antipathogen response of the model macroalga Delisea pulchra under the environmental conditions that promote the onset of disease. The study identified unique transcripts affiliated with stress response and signal transduction processes, and revealed the downregulation of genes coding for predicted protein metabolism, stress response, energy generation, and photosynthesis functions in the presence of the opportunistic pathogen. This repression of core cellular processes likely interferes with the macroalgal antipathogen response, leading to infection, tissue damage, and bleaching symptoms.
Article
Environmental Sciences
Fan Ling, Suhelen Egan, Yingrui Zhuang, Lirong Chang, Luyang Xiao, Qin Yang, Gaoge Wang
Summary: In this study, we investigated the dynamic shifts in the composition of the epibacterial communities of commercially farmed brown seaweed Saccharina japonica with disease progression. Our results showed that the alpha diversity was significantly higher in the control group than in the infected group. There was a significant shift in the composition and predicted functions of the epibacterial communities in both control and infected groups. Indicator species belonging to Stenotrophomonas, Pseudomonas and Sphingomona were significantly higher in the control group, while Vibrio, Pseudoalteromonas and Colwellia were keystone taxa in the infected group.
FRONTIERS IN MARINE SCIENCE
(2022)
Review
Microbiology
Jennifer Hudson, Suhelen Egan
Summary: Bacteria within the phylum Bacteroidota can cause devastating disease outbreaks in marine eukaryotic hosts, with Tenacibaculum and Aquimarina being the most common pathogens. These bacteria typically have an opportunistic lifestyle and can act as secondary pathogens or be involved in polymicrobial diseases. Environmental stressors, especially those affecting coral, macroalgae, and fish, are often associated with the diseases caused by Bacteroidota. Key virulence traits include the production of adhesins and host tissue-degrading enzymes.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Fisheries
Lara Parata, Joshua Noiney, Marwan E. Majzoub, Debashish Mazumder, Suhelen Egan, Jesmond Sammut
Summary: Subsistence freshwater fish farming in developing countries is growing rapidly, but many farmers still struggle with low productivity. This study compared two farming practices and found that using pelleted feed and NPK fertilization resulted in larger and healthier fish compared to using vegetables as supplementary feed. The addition of NPK improved the fish's ability to utilize commercial feed pellets, and the microbiota of fish reared with NPK positively correlated with growth and profitability. These findings have important implications for the health of subsistence fish farmers and the livelihoods of communities in Papua New Guinea.
Review
Biotechnology & Applied Microbiology
Jiasui Li, Florian Weinberger, Rocky de Nys, Torsten Thomas, Suhelen Egan
Summary: Eukaryotic hosts rely on microbial communities for their proper functioning, and manipulating these microbiota through beneficial microorganisms can enhance host performance and health. Seaweed beneficial microorganisms have been found to promote seaweed growth and development, as well as improve disease resistance. This knowledge can be applied to improve seaweed aquaculture and restoration practices. The challenges and opportunities of using seaweed beneficial microorganisms in aquaculture are discussed.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Jessica L. Bergman, Tayla Shaw, Suhelen Egan, Tracy D. Ainsworth
Summary: With advancements in sequencing techniques, there has been a rapid increase in studies on the microbiome in coral health and response to environmental change. However, methodological variations in DNA extraction protocols and tissue sampling can impact downstream analyses of microbial communities. Different studies have focused on whole organisms or specific microhabitats within coral, leading to variations in microbial data generated.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Mingyu Ma, Yingrui Zhuang, Lirong Chang, Luyang Xiao, Qin Lin, Qiying Qiu, Defu Chen, Suhelen Egan, Gaoge Wang
Summary: Microbiome manipulation is a way to mitigate diseases in aquaculture. A beneficial bacterium, Vibrio alginolyticus X-2, has been identified to significantly reduce the risk of bleaching disease in commercially farmed seaweed. This study provides insights into disease control in farmed Saccharina japonica through the application of beneficial bacteria.
Article
Nutrition & Dietetics
Hui Chen, Catherine Burke, Chantal Donovan, Alen Faiz, Sonia Saad, Brian G. Oliver
Summary: This study found that high-fat diet increased levels of triglycerides and non-esterified fatty acids in the blood, which were significantly reduced by e-vapour exposure. High-fat diet had a significant effect on microbial diversity, but there were no additional effects of e-vapour exposure.
Article
Biology
Hakim Ullah Wazir, Pooja Narang, Giulia Silvani, Christine Mehner, Kate Poole, Catherine Burke, Joshua Chou
Summary: With reusable rocket propulsion technology advancing, space tourism has become feasible at a cost-effective rate. Maintaining a balanced healthy microbiome is crucial for human survival and mission success during long-duration space missions, as the outer space environment can directly affect the human microbiome.