Review
Agriculture, Dairy & Animal Science
Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramirez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Summary: Microbiome studies in animal science using 16S rRNA gene sequencing are becoming more common. This review serves as a guide for animal scientists less familiar with this method, discussing common issues and considerations in planning such studies.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Microbiology
Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Summary: A high-throughput sequencing method was developed for profiling Pseudomonas species in soil microbiomes, identifying more species than 16S rRNA gene sequencing or cultivation. This method allows for tracing specific species of Pseudomonas and screening environmental samples for further isolation and exploitation.
Article
Biotechnology & Applied Microbiology
Dattatray S. Mongad, Nikeeta S. Chavan, Nitin P. Narwade, Kunal Dixit, Yogesh S. Shouche, Dhiraj P. Dhotre
Summary: 16S rRNA gene amplicon sequencing accurately characterizes microbial taxonomic abundances but lacks functional information. MicFunPred, a new tool, uses core genes to predict metagenomes, showing low False Positive Rate and performing faster with lower computational requirements compared to other tools.
Article
Agronomy
Svetlana B. Lysko, Olga A. Baturina, Natalia B. Naumova, Nadezhda A. Lescheva, Valentina I. Pleshakova, Marsel R. Kabilov
Summary: This study examined the effect of pectin prebiotics on the gut microbiota of chickens. The results showed that the prebiotic supplementation increased the abundance of Enterococcus and improved feed use efficiency and growth performance. The response of the microbiota to antibiotics showed more sex-related differential OTUs compared to the pectin prebiotic. Therefore, sex should be taken into account in interventional studies of gut microbiota.
Article
Agronomy
Natalia B. Naumova, Tatiana Y. Alikina, Natalia S. Zolotova, Alexey Konev, Valentina Pleshakova, Nadezhda A. Lescheva, Marsel R. Kabilov
Summary: The study found that feed enriched with probiotics can significantly reduce the presence of opportunistic pathogen Escherichia/Shigella, increase duck production performance, and enhance fecal microbial diversity.
Article
Fisheries
Christina Pavloudi, Maria Ioanna Tsertou, Efthimia Antonopoulou, Pantelis Katharios
Summary: Systemic granulomatosis is a mysterious disease affecting the important aquaculture fish species, Argyrosomus regius, and its etiology remains unknown. Through amplicon metagenomics analysis of the 16S rRNA gene in fish kidneys, it was found that all fish had similar bacterial communities. The presence of only three significantly enriched OTUs in sick individuals, none of which were known granuloma-causing species, supports the hypothesis of a non-infectious cause of this disease in this fish species.
Article
Microbiology
Wenke Zhang, Xiaoquan Fan, Haobo Shi, Jian Li, Mingqian Zhang, Jin Zhao, Xiaoquan Su
Summary: In this study, a comprehensive method called Qscore was proposed to evaluate the performance of 16S rRNA amplicons in microbial profiling. The method integrated factors such as amplification rate, taxonomic annotation, sequence type, and length. Evaluation of a wide range of microbe species and microbiomes showed that the Qscore-suggested parameters resulted in high precision in microbiome profiling. This study has significant implications for guiding future microbiome studies and enabling the reuse of massive sequence data.
MICROBIOLOGY SPECTRUM
(2023)
Article
Medicine, General & Internal
Amir Horev, Michael Brandwein, Avraham Vaknin, Yair Motro, Jacob Moran-Gilad
Summary: This study tracked the skin microbiome of patients with EB and found reduced bacterial diversity and increased staphylococcal carriage in these patients. Topical dressing may have a potential effect on the wound microbiome and contribute to skin healing.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Microbiology
Ezgi Ozkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Summary: LotuS2 is a lightweight and user-friendly pipeline for amplicon sequence analysis, offering high speed and precision, as well as improved data quality through extensive pre- and post-processing steps.
Article
Biology
Andrei A. Pochtovyi, Daria V. Vasina, Bakhtiyar I. Verdiev, Alexey M. Shchetinin, Anton G. Yuzhakov, Roman S. Ovchinnikov, Artem P. Tkachuk, Vladimir A. Gushchin, Alexander L. Gintsburg
Summary: This study analyzed the bioaerosol and surface microbiome of two subway stations in Moscow and found differences in microbiological and antibiotic-resistance profiles depending on the station. Differences between aerosol and surface bacterial communities were also found, highlighting the importance of diversified sampling during microbiome profiling of public areas.
Review
Biochemical Research Methods
Richa Bharti, Dominik G. Grimm
Summary: Analyzing the microbiome using next-generation sequencing techniques has improved our understanding of environmental microorganisms. However, analysis is affected by experimental conditions and downstream analysis, and new sequencing technologies can impact results. This work aims to review important workflows for sequencing data and provide best-practice protocols.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Konstantina Athanasopoulou, Panagiotis G. G. Adamopoulos, Andreas Scorilas
Summary: Over 10(14) symbiotic microorganisms in a healthy human body are responsible for important synthesis and support of the immune system. However, microbial deregulation can lead to various diseases. The human gastrointestinal tract is a favorable environment for diverse microbes. The gut microbiome, the largest microbiome community in the human body, has been extensively studied for its medical significance. Advances in sequencing techniques have enabled the detection of microbiomes and opened new avenues in studying human microbiota. The present review emphasizes the complexity of the gastrointestinal tract microbiome and its implications in cellular homeostasis and human diseases.
Article
Microbiology
Kayla M. Williamson, Brandie D. Wagner, Charles E. Robertson, Mark J. Stevens, Marci K. Sontag, Peter M. Mourani, J. Kirk Harris
Summary: The study aimed to increase the sensitivity of bacterial community analysis without impacting community composition or interfering with cluster formation during sequencing. The modified PCR protocol showed increased sensitivity in detecting bacterial communities in airway samples, crucial for studying the highly variable human airway microbiome.
Article
Immunology
Yuan Wang, Xuan Li, Shuntong Gu, Junhong Fu
Summary: This study found differences in the composition and function of the conjunctival and nasal microbiome in patients with allergic rhinoconjunctivitis (ARC) or allergic rhinitis (AR), suggesting a relationship between allergic conditions and the local microbiome.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Nutrition & Dietetics
Joana Rossell, Bjorn Brindefalk, Juan Antonio Baena-Fustegueras, Julia Peinado-Onsurbe, Klas Udekwu
EUROPEAN JOURNAL OF NUTRITION
(2020)
Article
Multidisciplinary Sciences
Asa Motiei, Bjorn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas Udekwu, Elena Gorokhova
Article
Immunology
Nuno Rufino de Sousa, Niklas Sandstrom, Lei Shen, Kathleen Hakansson, Rafaella Vezozzo, Klas Udekwu, Julio Croda, Antonio Gigliotti Rothfuchs
Article
Biochemistry & Molecular Biology
Axel Furevi, Jonas Stahle, Claudio Muheim, Spyridon Gkotzis, Klas Udekwu, Daniel O. Daley, Goran Widmalm
CARBOHYDRATE RESEARCH
(2020)
Article
Environmental Sciences
Stefano Bonaglia, Elias Broman, Bjorn Brindefalk, Erika Hedlund, Tomas Hjorth, Carl Rolff, Francisco J. A. Nascimento, Klas Udekwu, Jonas S. Gunnarsson
Article
Genetics & Heredity
Kari Oline Boifot, Jostein Gohli, Gunnar Skogan, Marius Dybwad
ENVIRONMENTAL MICROBIOME
(2020)
Article
Biochemistry & Molecular Biology
David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista A. Ryon, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Canas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Francesca De Filippis, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Dennis Gankin, Jonathan S. Gootenberg, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Jaden J. A. Hastings, Mark Hernandez, Gregorio Iraola, Soojin Jang, Andre Kahles, Frank J. Kelly, Kaymisha Knights, Nikos C. Kyrpides, Pawel P. Labaj, Patrick K. H. Lee, Marcus H. Y. Leung, Per O. Ljungdahl, Gabriella Mason-Buck, Ken McGrath, Cem Meydan, Emmanuel F. Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Marina Nieto-Caballero, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan Ozcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Ratsch, Lynn M. Schriml, Torsten Semmler, Osman U. Sezerman, Leming Shi, Tieliu Shi, Rania Siam, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Scott W. Tighe, Xinzhao Tong, Klas Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar Vassilev, Elena M. Vayndorf, Thirumalaisamy P. Velavan, Jun Wu, Maria M. Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E. Mason
Summary: This study establishes a global metagenomic atlas of urban microbial ecosystems, revealing a vast number of unknown microbial species and genetic elements, highlighting the distribution of antibiotic resistance genes in cities, and indicating the influence of geographical and climatic characteristics on urban microbial composition.
Article
Microbiology
M. H. Y. Leung, X. Tong, K. O. Boifot, D. Bezdan, D. J. Butler, D. C. Danko, J. Gohli, D. C. Green, M. T. Hernandez, F. J. Kelly, S. Levy, G. Mason-Buck, M. Nieto-Caballero, D. Syndercombe-Court, K. Udekwu, B. G. Young, C. E. Mason, M. Dybwad, P. K. H. Lee
Summary: The study found that city was the main factor influencing differences in the public transit air microbiome, with diverse taxa driving geography-specific functional potentials. Bacterial strains in different cities showed variations in genes related to resistance and other functions. Human skin, soil, and wastewater were identified as major presumptive sources of resistome in the public transit air, with a significant presence of resistance genes co-located with mobile genetic elements like plasmids. Geographical specificity played a key role in shaping the public transit air microbiome, highlighting the need for global efforts to better understand this built environment.
Article
Genetics & Heredity
Gabriela E. de Albuquerque, Bruno S. Moda, Marianna S. Serpa, Gabriela P. Branco, Alexandre Defelicibus, Isabella K. T. M. Takenaka, Maria G. de Amorim, Elizabeth C. Miola, Valquiria C. A. Martins, Katia L. Torres, Stephania M. Bezerra, Laura C. L. Claro, Adriane G. Pelosof, Claudia Z. Sztokfisz, Lais L. S. Abrantes, Felipe J. F. Coimbra, Luiz P. Kowalski, Fabio A. Alves, Stenio C. Zequi, Klas I. Udekwu, Israel T. Silva, Diana N. Nunes, Thais F. Bartelli, Emmanuel Dias-Neto
Summary: This study presents a targeted qPCR approach to determine the absolute and relative abundance of bacteria and fungi in different human tissue types. The results show that fungi are more abundant in stool and skin samples, while bacteria are more prevalent in stool, skin, oral swabs, saliva, and gastric fluids.
Article
Construction & Building Technology
Nuno Rufino de Sousa, Laura Steponaviciute, Lucille Margerie, Karolina Nissen, Midori Kjellin, Bjorn Reinius, Erik Salaneck, Klas Udekwu, Antonio Gigliotti Rothfuchs
Summary: This study detected aerosol transmission of SARS-CoV-2 in rooms occupied by COVID-19 patients in a hospital in Sweden and found infectious SARS-CoV-2 particles in the air. This suggests the need for revising existing infection control frameworks to include airborne transmission.
Letter
Construction & Building Technology
Nuno Rufino de Sousa, Laura Steponaviciute, Lucille Margerie, Karolina Nissen, Midori Kjellin, Bjorn Reinius, Erik Salaneck, Klas I. Udekwu, Antonio Gigliotti Rothfuchs
Article
Biochemistry & Molecular Biology
Axel Furevi, Klas Udekwu, Goran Widmalm
Summary: This study elucidates the structure of the O-antigen polysaccharide from Enteropathogenic Escherichia coli O125ac:H6 through NMR experiments and sugar analysis, confirming a branched pentasaccharide structure for the repeating unit. Additionally, by utilizing the CASPER program, the O-antigen structure of O125ab, composed of hexasaccharide repeating units, was established in a semi-automated manner. The close similarity between the O-antigen structures supports the presence of two subgroups within the E. coli O125 serogroup.
Article
Genetics & Heredity
Kari Oline Boifot, Jostein Gohli, Line Victoria Moen, Marius Dybwad
ENVIRONMENTAL MICROBIOME
(2020)
Article
Public, Environmental & Occupational Health
Jaime R. Cabrera-Pardo, Rolf Lood, Klas Udekwu, Gerardo Gonzalez-Rocha, Jose M. Munita, Josef D. Jarhult, Andres Opazo-Capurro