Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Article
Infectious Diseases
Rebecca Yee, Florian P. Breitwieser, Stephanie Hao, Belita N. A. Opene, Rachael E. Workman, Pranita D. Tamma, Jennifer Dien-Bard, Winston Timp, Patricia J. Simner
Summary: Antimicrobial resistance poses a threat to public health, necessitating efficient surveillance methods like metagenomic next-generation sequencing (mNGS). This approach showed promise in detecting multidrug-resistant organisms and provides a rapid and unbiased diagnostic tool for microbiome and resistome investigations.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Medicine, General & Internal
Zhonghui Ma, Su Yan, Haoxin Dong, Huifen Wang, Yonggang Luo, Xi Wang
Summary: Brain abscesses are associated with an increased long-term risk of new seizures and mortality, with common microorganisms including bacteria, fungi, and mycoplasma. We present a case of a 75-year-old man with a brain abscess caused by an oral pathogen, Prevotella denticola, where metagenomics sequencing was critical in determining targeted antibiotic therapy.
FRONTIERS IN MEDICINE
(2021)
Review
Cell Biology
Heloise Tudela, Sandrine P. Claus, Maya Saleh
Summary: The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, has a significant impact on health and disease. Keystone species, essential microbes for microbiota balance, play crucial roles in maintaining essential functions and their identification is crucial for the development of microbiome-based therapeutics. Understanding the functions of keystone species is a major step towards comprehending microbiome dynamics in disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
Review
Infectious Diseases
Caitlin Sande, Zoe J. Boston, Lindsay R. Kalan, Meghan B. Brennan
Summary: The use of molecular microbiology techniques for diagnosing infection complicating diabetic foot ulcers is still a concern, but studies on metagenomics and metatranscriptomics show promise in accelerating the development of diagnostic assays.
CURRENT INFECTIOUS DISEASE REPORTS
(2023)
Review
Biochemical Research Methods
Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin
Summary: The study of microbial communities relies on comparing metagenomic next-generation sequencing data sets, facing challenges such as species identification and quantification, computation of distances between samples, and identification of features associated with a phenotype. Solutions involve reference-based methods using a database of reference genomes and reference-free methods working directly on sequencing reads.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Immunology
Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen
Summary: This article discusses the gaps in traditional culture and introduces the utility of next-generation sequencing (NGS) in diagnosing and treating peri-prosthetic joint infections. It highlights the clinical benefits of using NGS compared to culture alone and emphasizes the potential of NGS in improving the yield of identifying infective organisms in challenging cases.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Kazuhiro Horiba, Yuka Torii, Toshihiko Okumura, Suguru Takeuchi, Takako Suzuki, Jun-Ichi Kawada, Hideki Muramatsu, Yoshiyuki Takahashi, Tomoo Ogi, Yoshinori Ito
Summary: This study used next-generation sequencing (NGS) to detect causative pathogens in patients with febrile neutropenia (FN). Results showed that NGS detected putative pathogens in some patients. Common bacteria from oral, skin, and gut flora were found in blood samples, suggesting microbiota translocation to the bloodstream.
OPEN FORUM INFECTIOUS DISEASES
(2021)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Immunology
Denver T. Niles, Paula A. Revell, Daniel Ruderfer, Lucila Marquez, J. Chase McNeil, Debra L. Palazzi
Summary: Plasma metagenomic next-generation sequencing (mNGS) has the potential to detect multiple organisms with a single test. The study found that mNGS testing had the highest clinical impact in immunocompromised patients with well-defined deep-seated infections. Further research is needed to evaluate the full range of clinical scenarios for which mNGS testing is beneficial.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2022)
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Article
Ecology
Maxim Rubin-Blum, Chakkiath Paul Antony, Lizbeth Sayavedra, Clara Martinez-Perez, Daniel Birgel, Joern Peckmann, Yu-Chen Wu, Paco Cardenas, Ian MacDonald, Yann Marcon, Heiko Sahling, Ute Hentschel, Nicole Dubilier
Article
Microbiology
Maxim Rubin-Blum, Nicole Dubilier, Manuel Kleiner
Article
Microbiology
Brandon K. B. Seah, Chakkiath Paul Antony, Bruno Huettel, Jan Zarzycki, Lennart Schada von Borzyskowski, Tobias J. Erb, Angela Kouris, Manuel Kleiner, Manuel Liebeke, Nicole Dubilier, Harald R. Gruber-Vodicka
Article
Microbiology
Harald R. Gruber-Vodicka, Nikolaus Leisch, Manuel Kleiner, Tjorven Hinzke, Manuel Liebeke, Margaret McFall-Ngai, Michael G. Hadfield, Nicole Dubilier
NATURE MICROBIOLOGY
(2019)
Article
Ecology
Adrien Assie, Nikolaus Leisch, Dimitri Meier, Harald Gruber-Vodicka, Halina E. Tegetmeyer, Anke Meyerdierks, Manuel Kleiner, Tjorven Hinzke, Samantha Joye, Matthew Saxton, Nicole Dubilier, Jillian M. Petersen
Article
Ecology
Devani Romero Picazo, Tal Dagan, Rebecca Ansorge, Jillian M. Petersen, Nicole Dubilier, Anne Kupczok
Article
Microbiology
Rebecca Ansorge, Stefano Romano, Lizbeth Sayavedra, Miguel Angel Gonzalez Porras, Anne Kupczok, Halina E. Tegetmeyer, Nicole Dubilier, Jillian Petersen
NATURE MICROBIOLOGY
(2019)
Article
Microbiology
Benedikt Geier, Emilia M. Sogin, Dolma Michellod, Moritz Janda, Mario Kompauer, Bernhard Spengler, Nicole Dubilier, Manuel Liebeke
NATURE MICROBIOLOGY
(2020)
Editorial Material
Microbiology
Emilia M. Sogin, Erik Puskas, Nicole Dubilier, Manuel Liebeke
Article
Microbiology
Samuel A. Vohsen, Kaitlin E. Anderson, Andrea M. Gade, Harald R. Gruber-Vodicka, Richard P. Dannenberg, Eslam O. Osman, Nicole Dubilier, Charles R. Fisher, Iliana B. Baums
Article
Ecology
Merle Uecker, Rebecca Ansorge, Yui Sato, Lizbeth Sayavedra, Corinna Breusing, Nicole Dubilier
Summary: The composition and diversity of animal microbiomes are influenced by various factors, with host traits, environment, and geographic location being important drivers. In deep-sea mussels, geographic location appears to play a larger role than host genetics or other factors in shaping the symbiont community.
Article
Biology
Maximilian Franke, Benedikt Geier, Jorg U. Hammel, Nicole Dubilier, Nikolaus Leisch
Summary: This study revealed that deep-sea bathymodiolin mussels gradually acquire symbionts during metamorphosis, with symbionts initially colonizing the gills before spreading to other epithelial tissues of the host. When symbiont densities in plantigrade larvae reached those of adults, the host's intestinal structure changed.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Dolma Michellod, Tanja Bien, Daniel Birgel, Marlene Violette, Manuel Kleiner, Sarah Fearn, Caroline Zeidler, Harald R. Gruber-Vodicka, Nicole Dubilier, Manuel Liebeke
Summary: Using various techniques, such as metabolite imaging and enzyme assays, we have discovered that gutless marine annelids synthesize the plant sterol sitosterol, which is commonly found in plants. This synthesis is facilitated by a noncanonical C-24 sterol methyltransferase, an enzyme that is essential for sitosterol synthesis in plants but not widely known in most animals. Our phylogenetic analyses also indicate that this enzyme is present in representatives of at least five animal phyla, suggesting that the synthesis of plant-like sterols is more common in animals than previously believed.
Article
Microbiology
Yui Sato, Juliane Wippler, Cecilia Wentrup, Tanja Woyke, Nicole Dubilier, Manuel Kleiner
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Yui Sato, Juliane Wippler, Cecilia Wentrup, Nicole Dubilier, Manuel Kleiner
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
