Article
Gastroenterology & Hepatology
Fergus W. J. Collins, Calum J. Walsh, Beatriz Gomez-Sala, Elena Guijarro-Garcia, David Stokes, Klara B. Jakobsdottir, Kristjan Kristjansson, Finlay Burns, Paul D. Cotter, Mary C. Rea, Colin Hill, R. Paul Ross
Summary: Shotgun metagenomic sequencing of the intestinal microbiome of 32 species of deep-sea fish across the Atlantic Ocean revealed extensive differences from previously identified microbes in reference databases. The constructed metagenome-assembled genomes (MAGs) demonstrate how these microbes have adapted to deep-sea life, with almost complete lack of acquired resistance genes to known antibiotics in many samples.
Review
Marine & Freshwater Biology
Beiyu Hu, Peng Xu, Liang Ma, Dongwei Chen, Jian Wang, Xin Dai, Li Huang, Wenbin Du
Summary: Microbes play a crucial role in influencing the Earth's environment, yet remain poorly understood due to limited capacity. The emerging technology of droplet microfluidics offers promising solutions for microbial studies, enabling high-throughput single-cell cultivation, screening, and sequencing. This review provides an overview of droplet microfluidics techniques for microbial research, focusing on critical steps in the microfluidic system and recent progress in microbiological applications.
MARINE LIFE SCIENCE & TECHNOLOGY
(2021)
Review
Chemistry, Analytical
Xiaoting Guo, Qiuxia Shen, Ziyu Chen, Ziyi He, Xianghua Yan
Summary: This review provides an overview of microfluidic technology for bacterial single-cell analysis in mammals. It discusses single-bacterial compartmentalization strategies and detection techniques in microfluidic systems, and highlights recent advances in single-bacterial microfluidics from nine aspects. It also discusses current challenges and future perspectives for improving microfluidic technology for bacterial single-cell analysis. This review will contribute to a better understanding of the evolutionary and functional diversity of mammalian microbiomes.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xiaobo Li, Yanqing Song, Xiuzhao Chen, Jianan Yin, Ping Wang, He Huang, Huabing Yin
Summary: The rapid spread of antibiotic resistance is a significant threat to global health. Evaluating drug combinations can help treat multidrug-resistant bacteria and prolong the effectiveness of existing antibiotics. This study uses single-cell microfluidics to rapidly evaluate the efficacy and mode of action of antibiotic combinations. The researchers discover the synergistic effect of combining berberine hydrochloride (BBH) and carbapenems (meropenem, MEM) or β-lactam antibiotics in treating multidrug-resistant Acinetobacter baumannii.
Article
Environmental Sciences
Animesh Tripathi, Dinesh Kumar, Priyank Chavda, Dalip Singh Rathore, Ramesh Pandit, Damer Blake, Fiona Tomley, Madhvi Joshi, Chaitanya G. Joshi, Suresh Kumar Dubey
Summary: Poultry farming in South and Southeast Asian economies is intensifying to meet the increasing demand for protein, but this intensification leads to increased use of antimicrobial drugs and the spread of antimicrobial resistance genes (ARGs), posing a threat to food chains. This study investigates the transmission of ARGs from chicken litter to soil and plants, and demonstrates that ARGs can be transmitted from litter to plant systems. The most common ARGs detected were cmx, ErmX, ErmF, lnuB, TEM-98, and TEM-99, and the common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. The findings highlight the risks posed to the environment by antimicrobial treatment of poultry and provide valuable knowledge for formulating intervention strategies to prevent ARGs transmission and improve understanding of the impacts on human and environmental health.
ENVIRONMENTAL POLLUTION
(2023)
Article
Microbiology
Nana Wei, Jinmiao Lu, Yi Dong, Shibo Li
Summary: This study investigated the microbial community and antibiotic resistome in wild tick species. The results showed that the microbial composition is variable, with Proteobacteria and Bacteroidetes being the dominant phyla. A total of 100 different antibiotic resistance genes (ARGs) across 12 antibiotic classes were identified, with aminoglycosides, multidrug, macrolide-clinolamide-streptogramin B, and tetracycline resistance genes being the most dominant. Network analysis revealed potential host genera for different ARGs. This study provides a comprehensive overview of the diversity and abundance of ARGs in wild ticks, highlighting their potential role as disseminators of ARGs into the environment and vertebrate hosts.
Review
Oncology
Mahmoud Labib, Shana O. Kelley
Summary: Analysis of circulating tumor cells provides valuable insights in precision oncology, revealing associations between CTCs molecular profiles and tumor response to therapy. However, current limitations hinder the widespread clinical implementation of CTCs, suggesting the need for further research and advanced technologies.
MOLECULAR ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Leland B. Hyman, Clare R. Christopher, Philip A. Romero
Summary: Experimental methods focusing on individual properties of single cells have highlighted the significance of cell-to-cell variability in biological processes. SNAPD, a technology for single-cell nucleic acid profiling in droplets, provides a rapid, high-throughput approach for analyzing transcriptional markers in cell populations, allowing for cell classification and quantification in heterogeneous samples.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Emily Pope, Christopher Cartmell, Bradley Haltli, Ali Ahmadi, Russell G. G. Kerr
Summary: This study demonstrates that microencapsulation followed by in situ incubation can improve bacterial recovery from marine sediments by increasing abundance, viability, and diversity. Agarose encapsulation promotes higher cell viability during in situ incubation and recovers greater bacterial diversity compared to simple resuspension. The results suggest that agarose encapsulation coupled with in situ incubation facilitates the cultivation and improved recovery of bacteria from marine sediments.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Immunology
Winston E. Anthony, Carey-Ann D. Burnham, Gautam Dantas, Jennie H. Kwon
Summary: This review discusses the gut as a reservoir for antimicrobial resistance and pathogen colonization, with a focus on beta-lactam and plasmid-mediated quinolone resistance. It also explores the use of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome, as well as the potential for future microbiome-directed methods for detecting and preventing infections.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Ecology
Melanie Maria Obermeier, Wisnu Adi Wicaksono, Julian Taffner, Alessandro Bergna, Anja Poehlein, Tomislav Cernava, Stefanie Lindstaedt, Mario Lovric, Christina Andrea Mueller Bogota, Gabriele Berg
Summary: Our research identified a diverse pool of resistance determinants in the microbiome associated with Sphagnum moss, showing resistance to a broad range of 29 antibiotics including natural and synthetic compounds. Multi-resistance was frequently observed among bacterial isolates, and a new class A beta-lactamase Mm3 was discovered. This highlights the ecological link between natural and clinically relevant resistomes and emphasizes that diverse resistomes are a characteristic of plant-associated microbial communities.
Article
Immunology
S. Aishwarya, K. Gunasekaran, P. Senthil Kumar, Arshiya Begum, Evangeline Shantha, V Jeevitha, K. Veena Gayathri
Summary: The structure and functions of microbial communities in river ecosystems play a crucial role in determining the health, quality, and anthropogenic conditions of the rivers. Specific bacteria present in rivers, such as Arcobacter spp, Escherichia spp, and Campylobacters spp, can indicate poor water quality. The current study utilized metagenomic and metatranscriptomic approaches to uncover the diverse microbial taxonomy in the Cooum river, revealing potential antimicrobial and metal resistance mechanisms.
MICROBIAL PATHOGENESIS
(2021)
Article
Biophysics
Yi Zhang, Nurhidayah Binte Mohamed Yazid, Pei-Yun Ho, Xuyang Hu, Songlin Chen, Shawn Vasoo, Pojchanun Kanitthamniyom
Summary: This study presents an automated magnetic digital microfluidics-based platform, called DropCarba, for the detection of carbapenemase-producing Gram-negative bacilli (CPGNB). The platform simplifies the testing process, improves consistency, and has comparable results to the standard Carba NP test. It provides a valuable contribution to combating antibiotic resistance.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Joseph de Rutte, Robert Dimatteo, Maani M. Archang, Mark van Zee, Doyeon Koo, Sohyung Lee, Allison C. Sharrow, Patrick J. Krohl, Michael Mellody, Sheldon Zhu, James Eichenbaum, Monika Kizerwetter, Shreya Udani, Kyung Ha, Richard C. Willson, Andrea L. Bertozzi, Jamie B. Spangler, Robert Damoiseaux, Dino Di Carlo
Summary: Techniques to analyze and sort single cells based on functional outputs have the potential to transform cellular biology and accelerate the development of cell and antibody therapies. This study describes a method to fabricate chemically functionalized microcontainers, called nanovials, for sorting single cells based on their secreted products. The nanovials can be easily used with commonly accessible laboratory infrastructure and allow high-throughput screening of cells.
Article
Biotechnology & Applied Microbiology
Julian Schmitz, Sarah Tauber, Christoph Westerwalbesloh, Eric von Lieres, Thomas Noll, Alexander Grunberger
Summary: This study introduces a microfluidic tool for single-cell cultivation of mammalian suspension cells, allowing for analysis of cellular heterogeneity and rare cell events. By cultivating CHO-K1 cells at a single-cell level, diverse growth and division behaviors, as well as unique cellular events, were observed.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Microbiology
Gleb Yu Fisunov, Olga Pobeguts, Valentina G. Ladygina, Alexandr Zubov, Mariya A. Galyamina, Sergey Kovalchuk, Rustam K. Ziganshin, Daria Evsyutina, Daria S. Matyushkina, Ivan O. Butenko, Olga N. Bukato, Vladimir A. Veselovsky, Tatiana A. Semashko, Ksenia M. Klimina, Galina A. Levina, Olga Barhatova, Irina Rakovskaya
Summary: The study reveals the physiological differences between micro-colonies (MCs) and typical colonies (TCs) of Mycoplasma hominis through proteomic analysis. MCs preferential utilization of deoxyribonucleosides as an energy source and their reorganization of energy metabolism contributes to their survival and antibiotic resistance under stress conditions. This research provides insights into the formation and growth pathways of MCs and their significance in the context of survival and resistance.
JOURNAL OF MEDICAL MICROBIOLOGY
(2022)
Article
Biology
Anastasiia Rusanova, Victor Fedorchuk, Stepan Toshchakov, Svetlana Dubiley, Dmitry Sutormin
Summary: This study provides insights into the metagenomics of three cold-water sponge species from the White Sea, revealing species-specific bacterial and viral communities associated with the sponges. The study also highlights the abundance of virus-host interactions within the sponge-associated community and the occurrence of viral exchanges between communities.
Article
Biochemistry & Molecular Biology
Vera A. Alferova, Tinashe P. Maviza, Mikhail V. Biryukov, Yuliya V. Zakalyukina, Vladimir I. Polshakov, Petr V. Sergiev, Vladimir A. Korshun, Ilya A. Osterman
Summary: Recently discovered aromatic polyketide tetracenomycins are potent inhibitors of protein synthesis, with a unique binding site located within the tunnel of the large ribosomal subunit. We report the isolation and structure elucidation of a novel tetracenomycin congener, O4-Me-tetracenomycin C, which is isomeric to tetracenomycin X. However, unlike tetracenomycin X, O4-Me-tetracenomycin C showed no antimicrobial activity and failed to inhibit protein synthesis in vitro. Structural alignment of tetracenomycins revealed the crucial role of the 4-hydroxyl group. These findings are important for the development of semi-synthetic tetracenomycins as potential antibacterials.
Article
Biochemistry & Molecular Biology
Anna Gladkikh, Ekaterina Klyuchnikova, Polina Pavlova, Valeriya Sbarzaglia, Nadezhda Tsyganova, Margarita Popova, Tatiana Arbuzova, Alena Sharova, Edward Ramsay, Andrei Samoilov, Vladimir Dedkov, Areg Totolian
Summary: This study compares three different protocols for SARS-CoV-2 whole genome sequencing library construction and finds that the custom panel method has suitable results and predictable output for the epidemiological surveillance of SARS-CoV-2 variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Infectious Diseases
Julia A. Pavlova, Andrey G. Tereshchenkov, Pavel A. Nazarov, Dmitrii A. Lukianov, Dmitry A. Skvortsov, Vladimir I. Polshakov, Byasilya F. Vasilieva, Olga V. Efremenkova, Mikhail Y. Kaiumov, Alena Paleskava, Andrey L. Konevega, Olga A. Dontsova, Ilya A. Osterman, Alexey A. Bogdanov, Natalia V. Sumbatyan
Summary: To improve the properties of antimicrobial compounds, new conjugates were synthesized and studied, which consisted of two different biologically active agents in a single chimeric molecule based on chloramphenicol and a hydrophobic cation. These conjugates, named CAM-Cn-BER, effectively bound to the bacterial ribosome and inhibited protein synthesis, similar to chloramphenicol. CAM-C8-BER displayed selective inhibition of Gram-positive bacteria and acted on both the ribosome and the cell membrane. Moreover, CAM-Cn-BERs did not inhibit eukaryotic translation and were non-toxic to eukaryotic cells.
Correction
Microbiology
Yuliya V. Zakalyukina, Ilya A. Osterman, Jacqueline Wolf, Meina Neumann-Schaal, Imen Nouioui, Mikhail V. Biryukov
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maria Kornienko, Dmitry Bespiatykh, Maja Malakhova, Roman Gorodnichev, Nikita Kuptsov, Egor Shitikov
Summary: Phage therapy is a hopeful approach to combat multidrug-resistant bacteria. However, it requires the isolation of new phages or the search for suitable phages in existing libraries. This study proposes a simple PCR method to differentiate between two families of Staphylococcus phages and eleven genera of Klebsiella phages, allowing for rapid screening and identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Roman B. Gorodnichev, Maria A. Kornienko, Maja V. Malakhova, Dmitry A. Bespiatykh, Valentin A. Manuvera, Oksana V. Selezneva, Vladimir A. Veselovsky, Dmitry V. Bagrov, Marina V. Zaychikova, Veronika A. Osnach, Anna V. Shabalina, Oleg V. Goloshchapov, Julia A. Bespyatykh, Anna S. Dolgova, Egor A. Shitikov
Summary: To address the crisis of Klebsiella pneumoniae infections caused by drug-resistant strains, new approaches to antimicrobial therapy, such as using phages or phage derivatives, need to be developed. This study describes the first K. pneumoniae phage from the Zobellviridae family, which was isolated from river water and demonstrates lytic activity against K. pneumoniae strains with the KL20 capsule type. The phage's receptor-binding protein was identified as a polysaccharide depolymerase, showing promise for using depolymerases in antimicrobial therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Ivan Smirnov, Alexey Belogurov Jr, Andrey Golovin, Alexey Stepanov, Hongkai Zhang, G. Michael Blackburn, Alexander Gabibov
Summary: The maturation of B cells leads to the synthesis of highly evolved immunoglobulins (Igs) that enable efficient antigen-antibody recognition. We discuss a non-opportunistic, combinatorial concept of maturation of Igs in silico for the production of artificially-evolved immunocatalysts. Recent breakthroughs in single B cell selection, combinatorial approaches powered by library screening, structural computing and machine learning, and QM/MM evaluations of catalytic reactions provide an optimistic prospect for more effective immunoglobulin-derived catalytic templates and a purely robotic selection process. The synergy of these approaches enables catalytic antibodies to become a great prospect for biomedical purposes, including therapeutic antibodies and catalytic Chimeric Antigen Receptors (catCARs) with controllable pharmacokinetic parameters.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Microbiology
Dmitrii Y. Y. Travin, Romain Jouan, Armelle Vigouroux, Satomi Inaba-Inoue, Joy Lachat, Fazal Haq, Tatiana Timchenko, Dmitry Sutormin, Svetlana Dubiley, Konstantinos Beis, Solange Morera, Konstantin Severinov, Peter Mergaert
Summary: The peptide antibiotic Phazolicin (PHZ) exhibits low resistance in Sinorhizobium meliloti due to its dual-entry mode through two different peptide transporters. This finding makes PHZ an attractive option for the development of biocontrol agents in agriculture.
Article
Ecology
Danil V. V. Krivonos, Dmitry N. N. Konanov, Elena N. N. Ilina
Summary: The study of individual fungi and their communities is important in modern biology as they can be both beneficial producers and harmful pathogens. Functional capabilities of fungi are determined by gene content, which is often obtained through whole genome sequencing. However, whole genome sequencing of fungi is not commonly done, and amplicon sequencing of ITS region does not provide functional annotation. Here, we introduce FunFun, a tool that evaluates gene content from ITS sequencing data using a modified K-nearest neighbors algorithm. FunFun can be used to compare and estimate functional capabilities of fungi and accurately predict the most variable functions.
ECOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Evgenii I. I. Olekhnovich, Artem B. B. Ivanov, Anna A. A. Babkina, Arseniy A. A. Sokolov, Vladimir I. I. Ulyantsev, Dmitry E. E. Fedorov, Elena N. N. Ilina
Summary: In this study, a list of potentially beneficial bacteria associated with melanoma immunotherapy responsiveness was compiled. Functional biomarkers of immunotherapy responsiveness were also identified and found to be dispersed among different bacterial species. These findings contribute to understanding the relationship between gut microbiome composition and treatment response, and have implications for the development of diagnostic tests and recommendations for gut microbiome correction in cancer immunotherapy.
Article
Pharmacology & Pharmacy
Kseniya Shapovalova, Georgy Zatonsky, Natalia Grammatikova, Ilya Osterman, Elizaveta Razumova, Andrey Shchekotikhin, Anna Tevyashova
Summary: Aminoglycosides, one of the earliest antibiotics used clinically, still hold promise for the development of new antibacterial agents. We synthesized 6''-deoxykanamycin A analogues and found that introducing guanidine residues improved their activity against S. aureus. Furthermore, these modified kanamycin A derivatives showed reduced susceptibility to resistance mechanisms associated with mutations of elongation factor G.
Article
Microbiology
Shao-Wei Liu, Xiao-Xu Zhai, Di Liu, Yu-Yu Liu, Li-Ying Sui, Ke-Ke Luo, Qin Yang, Fei-Na Li, Arina A. Nikandrova, Arina N. Imamutdinova, Dmitrii A. Lukianov, Ilya A. Osterman, Petr V. Sergiev, Ben-Yin Zhang, De-Jun Zhang, Chun-Mei Xue, Cheng-Hang Sun
Summary: This study investigates the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of saline lakes on the Northern Tibetan Plateau. Through the use of metabolomics and genomics approaches, potential bioactive compounds were rapidly identified, including potential novel anthracycline compounds.
Review
Biochemistry & Molecular Biology
J. A. Buyuklyan, Yu. V. Zakalyukina, I. A. Osterman, M. V. Biryukov
Summary: Representatives of the phylum Actinomycetota are important sources of secondary metabolites, including antibiotics. However, the production of these metabolites in laboratory conditions is low and there is a continuous rediscovery of known antibiotics, making new molecules harder to find. Established approaches to increase antibiotic production have limitations and are not always successful. Genetic engineering technologies, such as mutagenesis-based genome editing, offer a more efficient way to control and increase the production of target metabolites.
