Article
Genetics & Heredity
Elisabetta Notario, Grazia Visci, Bruno Fosso, Carmela Gissi, Nina Tanaskovic, Maria Rescigno, Marinella Marzano, Graziano Pesole
Summary: The 16S rRNA amplicon-based sequencing approach is commonly used and cost-effective for microbiome profiling. This study compared different methods and found that the full-length approach has the best discriminatory power for microbiome taxonomic characterization.
Article
Multidisciplinary Sciences
Rachel Gilroy, Joy Leng, Anuradha Ravi, Evelien M. Adriaenssens, Aharon Oren, Dave Baker, Roberto M. La Ragione, Christopher Proudman, Mark J. Pallen
Summary: By using metagenomic sequencing on thoroughbred equine faecal samples, this study provides new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets serve as an important resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.
Review
Microbiology
Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, Andre Karch, Nicole Ruebsamen
Summary: Reproducibility in microbiome studies is hindered by a lack of consensus on data analysis strategies. The complex nature of microbiome data, combined with increasingly sophisticated research questions, requires more advanced analytical methods. Current analysis strategies in microbiome studies show significant heterogeneity, particularly in differential abundance testing, indicating a need for better guidance in analyzing increasingly complex research questions.
Article
Health Care Sciences & Services
Souad Kartti, Houda Bendani, Nasma Boumajdi, El Mehdi Bouricha, Oumaima Zarrik, Hajar EL Agouri, Mohamed Fokar, Youssef Aghlallou, Rachid EL Jaoudi, Lahcen Belyamani, Basma Elkhannoussi, Azeddine Ibrahimi
Summary: This study analyzed the differences in bacterial composition between tumor and adjacent tissues in breast cancer patients in Morocco. The results showed that tumor tissues had a higher abundance of Bacilli and Actinobacteria, while adjacent tissues had a higher abundance of Gammaproteobacteria. Additionally, different microbial communities were identified in different breast cancer subtypes. These findings have implications for diagnosis and treatment strategies for breast cancer.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
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
Biotechnology & Applied Microbiology
Wirulda Pootakham, Wuttichai Mhuantong, Thippawan Yoocha, Duangjai Sangsrakru, Wasitthee Kongkachana, Chutima Sonthirod, Chaiwat Naktang, Nukoon Jomchai, Sonicha U-Thoomporn, Thammasak Yeemin, Sittiporn Pengsakun, Makamas Sutthacheep, Sithichoke Tangphatsornruang
Summary: This study investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, revealing that host species was a factor influencing the structure and composition of dinoflagellate communities. Different coral hosts were associated with different microbial taxa, and full-length 16S rRNA sequences demonstrated superior performance in achieving species-resolution taxonomic classification of coral-associated microbiota.
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.
Review
Microbiology
Imane Allali, Regina E. Abotsi, Lemese Ah. Tow, Lehana Thabane, Heather J. Zar, Nicola M. Mulder, Mark P. Nicol
Summary: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. Local leadership, capacity building, intra-continental collaboration, and national government investment are needed in microbiome research within Africa.
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.
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
Aleksandra Stupak, Wojciech Kwasniewski
Summary: The microbiome is of interest due to its potential influence on human illnesses. This review focuses on the methodologies and understanding of the functional microbiome in pregnancy outcomes. Research suggests that microbiome dysbiosis may be associated with antenatal illnesses such as fetal growth restriction and preeclampsia.
Article
Biotechnology & Applied Microbiology
Lauren M. O'Connell, Thomas Blouin, Ashlyn Soule, Robert A. Burne, Marcelle M. Nascimento, Vincent P. Richards
Summary: The microbiota associated with dental caries is still not fully understood. This study aimed to develop a more reliable method for identifying oral streptococci at the species level. The results showed that the newly developed 30S-S11 rRNA gene locus provided improved taxonomic resolution over the traditional 16S rRNA V4 approach. Additionally, different amplicon sequence variants within a species were found to vary in abundance at different stages of caries progression, suggesting distinct roles of strains within a single species in health and disease.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Nutrition & Dietetics
Mariona Pinart, Andreas Doetsch, Kristina Schlicht, Matthias Laudes, Jildau Bouwman, Sofia K. Forslund, Tobias Pischon, Katharina Nimptsch
Summary: Despite some studies finding lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.
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)
Article
Veterinary Sciences
Asha M. Miles, Jessica A. A. McArt, Svetlana F. Lima, Rafael C. Neves, Erika Ganda
Summary: This study investigated the correlation between the gut microbiome and the development of hyperketonemia in early lactation dairy cows, as well as identified potential microbial features related to health status. The results revealed no differences in the fecal microbiomes among health groups, while significant differences were observed in the rumen microbiomes between CON and HYK cows. Interestingly, highly similar microbiome composition was found in the rumen and fecal samples of C-HYK cows, suggesting that these initially healthy cows showed similar microbial composition after the onset of hyperketonemia. It was concluded that hyperketonemia may not be greatly influenced by gut microbial composition, and further studies are needed to explore the exact mechanisms involved.
BMC VETERINARY RESEARCH
(2022)
Article
Pathology
Sander van Boheemen, Anneloes L. van Rijn, Nikos Pappas, Ellen C. Carbo, Ruben H. P. Vorderman, Igor Sidorov, Peter J. van't Hof, Hailiang Mei, Eric C. J. Claas, Aloys C. M. Kroes, Jutte J. C. de Vries
JOURNAL OF MOLECULAR DIAGNOSTICS
(2020)
Article
Oncology
Wibowo Arindrarto, Daniel M. Borras, Ruben A. L. de Groen, Redmar R. van den Berg, Irene J. Locher, Saskia A. M. E. van Diessen, Rosalie van der Holst, Edith D. van der Meijden, M. Willy Honders, Rick H. de Leeuw, Wina Verlaat, Inge Jedema, Wilma G. M. Kroes, Jeroen Knijnenburg, Tom van Wezel, Joost S. P. Vermaat, Peter J. M. Valk, Bart Janssen, Peter de Knijff, Cornelis A. M. van Bergen, Erik B. van den Akker, Peter A. C. 't Hoen, Szymon M. Kielbasa, Jeroen F. J. Laros, Marieke Griffioen, Hendrik Veelken
Summary: The study established whole transcriptome RNA sequencing as a comprehensive platform for AML diagnostics by developing HAMLET, a bioinformatics pipeline that accurately detects fusion genes, small variants, and tandem duplications. HAMLET has the potential to provide accurate diagnostic information relevant for AML classification, risk assessment, and targeted therapy on a single technology platform.
Article
Multidisciplinary Sciences
Friederike Ehrhart, Annika Jacobsen, Maria Rigau, Mattia Bosio, Rajaram Kaliyaperumal, Jeroen F. J. Laros, Egon L. Willighagen, Alfonso Valencia, Marco Roos, Salvador Capella-Gutierrez, Leopold M. G. Curfs, Chris T. Evelo
Summary: Research on MECP2 in Rett syndrome can improve understanding of disease mechanisms and faster diagnosis of variants, but the lack of interoperability between genotype-phenotype databases currently hinders this process. Integrating a large amount of MECP2 variant data revealed variants that can cause both RTT and be benign, indicating additional factors contributing to disease development in these cases.
Article
Biochemical Research Methods
Mihai Lefter, Jonathan K. Vis, Martijn Vermaat, Johan T. den Dunnen, Peter E. M. Taschner, Jeroen F. J. Laros
Summary: The Human Genome Variation Society provides guidelines on accurately describing genetic variants, with the Mutalyzer tool suite being able to automatically apply these guidelines for users to check and correct their descriptions. Mutalyzer has successfully processed over 133 million descriptions, with around 50% being reported as correct and able to automatically correct descriptions for approximately 7% of cases.
Article
Infectious Diseases
Esther van Kleef, Cornelia C. H. Wielders, Leo M. Schouls, Sabiena G. Feenstra, Cees M. P. M. Hertogh, Marc J. M. Bonten, Yolanda van Weert, Alma Tostmann, Mariken van der Lubben, Sabine C. de Greeff
Summary: The study in Dutch LTCFs showed an estimated prevalence of 8.3% for ESBL-E rectal carriage, mainly observed in E. coli with prevalence of bla(CTX-M-15) and bla(CTX-M-27). No CPE were found in the study. Genetic clusters were identified in more than half of high ESBL-positive LTCFs, indicating potential institutional clonal transmission.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Medicine, Research & Experimental
Darina Sikrova, Vlad A. Cadar, Yavuz Ariyurek, Jeroen F. J. Laros, Judit Balog, Silvere M. van der Maarel
Summary: This study presents a strategy for mutagenesis of the somatic DUX4 polyadenylation signal using adenine base editing in immortalized myoblasts from FSHD-affected individuals, leading to downregulation of DUX4 mRNA and its target genes. These findings highlight the potential therapeutic target of the somatic DUX4 polyadenylation signal and represent the initial step towards clinical application of the CRISPR-Cas9 base editing platform for FSHD gene therapy.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Gastroenterology & Hepatology
Sam Nooij, Quinten R. Ducarmon, Jeroen F. J. Laros, Romy D. Zwittink, Jason M. Norman, Wiep Klaas Smits, Hein W. Verspaget, Josbert J. Keller, Elisabeth M. Terveer, Ed J. Kuijper
Summary: The study found that pks+ E coli was more prevalent and abundant in patients with rCDI, and FMT played a role in the persistence or eradication of pks+ E coli in patients. However, transmission of pks+ E coli from donors to patients is unlikely.
Article
Biotechnology & Applied Microbiology
L. D. Bertola, M. Vermaat, F. Lesilau, M. Chege, P. N. Tumenta, E. A. Sogbohossou, O. D. Schaap, H. Bauer, B. D. Patterson, P. A. White, H. H. de Iongh, J. F. J. Laros, K. Vrieling
Summary: This study used low-depth whole genome sequencing to analyze ten lions sampled across their geographic range, resulting in the discovery of over 150,000 single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed the split between northern and southern populations, as well as four population clusters on a local scale. A SNP panel was designed and tested on over 200 lions, allowing individuals to be assigned to one of the four major clades and providing detailed delineation of these clades.
Article
Multidisciplinary Sciences
K. Joeri van der Velde, Gurnoor Singh, Rajaram Kaliyaperumal, Xiaofeng Liao, Sander de Ridder, Susanne Rebers, Hindrik H. D. Kerstens, Fernanda de Andrade, Jeroen van Reeuwijk, Fini E. De Gruyter, Saskia Hiltemann, Maarten Ligtvoet, Marjan M. Weiss, Hanneke W. M. van Deutekom, Anne M. L. Jansen, Andrew P. Stubbs, Lisenka E. L. M. Vissers, Jeroen F. J. Laros, Esther van Enckevort, Daphne Stemkens, Peter A. C. t Hoen, Jeroen A. M. Belien, Marielle E. van Gijn, Morris A. Swertz
Summary: FAIR Genomes aims to facilitate the reuse of genomic data by developing metadata standards and providing templates for data entry and programmatic interfaces. It addresses the challenge of storing and sharing genomic data by offering a semantic schema for data descriptions. With FAIR Genomes, rare disease diagnosis and personalized medicine research can be enhanced.
Article
Biochemical Research Methods
Rob Marissen, Madhushri S. Varunjikar, Jeroen F. J. Laros, Josef D. Rasinger, Benjamin A. Neely, Magnus Palmblad
Summary: In this paper, the authors present an update to a method and software tool for species identification based on mass spectrometry data. The method has been widely used in various applications and now includes a new metric and graphical user interface.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters, Jeroen F. J. Laros
Summary: In this study, a set of Boolean relations is introduced to comprehensively classify the relations of every pair of variants by considering all minimal alignments. An efficient algorithm is presented to compute these relations, with a novel method to compute all minimal alignments within the best theoretical complexity bounds. The study demonstrates the commonness and complexity of these relations for variants of the CFTR gene in dbSNP. Additionally, an approach for storing and indexing variants in a database is proposed, enabling efficient querying for all these relations.
Article
Ecology
Jose L. Lopez, Arista Fourie, Sanne W. M. Poppeliers, Nikolaos Pappas, Juan J. Sanchez-Gil, Ronnie de Jonge, Bas E. Dutilh
Summary: The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions.
Meeting Abstract
Biochemistry & Molecular Biology
Kasper Joeri van der Velde, Gurnoor Singh, XiaoFeng Liao, Rajaram Kaliyaperumal, Daphne Stemkens, Esther van Enckevort, Susanne Rebers, Katy Wolstencroft, Sander de Ridder, Terry Vrijenhoek, Fernanda de Andrade, Anna Niehues, Hindrik H. D. Kerstens, Annika Jacobsen, Bart de Koning, Jeroen van Reeuwijk, Kim Elsink, Christine Staiger, Joris van Montfrans, Erik van Iperen, Nine Knoers, Stefan Willems, Wendy van Zelst-Stams, Helger Ijntema, Edwin Cuppen, Lieneke Steeghs, Salome Scholtens, Leon Mei, Patrick Kemmeren, Marco Roos, Cor Oosterwijk, Marjan Weiss, Andrew Stubbs, Peter A. C. tHoen, Jeroen Laros, Jeroen A. M. Belien, Marielle E. van Gijn, Morris A. Swertz
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Amy H. J. Chan, Michael G. Gardner, Adrian Linacre
Summary: We report the detection and visualisation of latent DNA from pangolin scales using a nucleic acid staining dye, and propose that this method is invaluable in wildlife forensic science.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Fernanda M. Garcia, Raquel S. R. Trabach, Victor S. Stange, Bruno Cancian, Alexia S. S. Zetum, Matheus C. Casotti, Flavia I. V. Errera, Elizeu F. de Carvalho, Debora D. Meira, Iuri D. Louro
Summary: This study found that the population of Espirito Santo, Brazil is genetically closer to the Italian population based on the analysis of STR markers on the X chromosome.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Zhiyong Liu, Jiajun Liu, Jiaojiao Geng, Enlin Wu, Jianzhang Zhu, Bin Cong, Riga Wu, Hongyu Sun
Summary: Microorganisms can serve as potential markers for identifying body fluids and tissues in forensic genetics. This study explored the use of metatranscriptomics to characterize common forensic samples and investigated the potential application of metatranscriptomics in forensic science. The results demonstrated high alpha diversity in saliva and skin samples, and the use of machine learning models showed that microbial RNA-based methods could be applied for forensic body fluid/tissue identification. Overall, this study provides insights into the role of metatranscriptomics in forensic science and its potential for microbe-based individual identification.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Guro Dorum, Nadescha Viviane Haenggi, Dario Burri, Yael Marti, Regine Banemann, Galina Kulstein, Cornelius Courts, Annica Gosch, Thorsten Hadrys, Cordula Haas, Jacqueline Neubauer
Summary: RNA has gained attention in forensic field for predicting biological age. This study used RNA-Seq data to search for markers associated with age and presented two candidate marker lists.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Michele Di Nunzio, Carme Barrot-Feixat, David Gangitano
Summary: This study developed five SNaPshotTM assays for nine chloroplast markers to differentiate between marijuana crop type and hemp crop type. The testing of 122 cannabis samples successfully distinguished between marijuana and hemp, and genetic differences between different groups based on biogeographical origin and crop type were observed. Phylogenetic analysis and principal component analysis provided valuable information about the genetic relationship and differentiation between different cannabis samples.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Genetics & Heredity
Katherine B. Gettings, Martin Bodner, Lisa A. Borsuk, Jonathan L. King, David Ballard, Walther Parson, Corina C. G. Benschop, Claus Borsting, Bruce Budowle, John M. Butler, Kristiaan J. van der Gaag, Peter Gill, Leonor Gusmao, Douglas R. Hares, Jerry Hoogenboom, Jodi Irwin, Lourdes Prieto, Peter M. Schneider, Marielle Vennemann, Christopher Phillips
Summary: The DNA Commission of the ISFG has developed nomenclature recommendations for STR sequences, incorporating research findings and providing guidance for interlaboratory comparisons and the integration of new markers into investigative databases.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)