Article
Fisheries
Socorro Toxqui-Rodriguez, Fernando Naya-Catala, Ariadna Sitja-Bobadilla, M. Carla Piazzon, Jaume Perez-Sanchez
Summary: This study compared different sequencing platforms for microbial characterization in fish gut mucosal samples. The results showed that MinION is a reliable and accurate tool for assessing intestinal bacteria communities, with good correlation with Illumina results. However, less abundant but biologically important taxa may be masked compared to Illumina sequencing.
Article
Immunology
Birgit Fritz, Edita Paschko, Wayne Young, Daniel Boehringer, Siegfried Wahl, Focke Ziemssen, Markus Egert
Summary: Slit lamps are commonly used for examining numerous patients and are often contaminated with bacteria from human skin, mucosa, and possibly eyes. The study showed a diverse bacterial microbiota on slit lamps, emphasizing the importance of thorough cleaning and disinfection to prevent infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Yu-Kun Zhang, Qian Zhang, Yu-Liuming Wang, Wei-Yuan Zhang, Han-Qing Hu, Hong-Yu Wu, Xiang-Zong Sheng, Kang-Jia Luo, Hao Zhang, Meng Wang, Rui Huang, Gui-Yu Wang
Summary: This study revealed differences in intestinal microbiota composition among groups of CRC patients, young volunteers, and old volunteers. The enrichment of specific bacteria in different age groups and in CRC patients suggests potential protective or tumorigenic roles, highlighting the importance of gut bacteria in colorectal cancer.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Environmental Sciences
Adithya Govindarajan, Mary Crum, Jay Adolacion, Amin Kiaghadi, Edgar Acuna-Gonzalez, Hanadi S. Rifai, Richard C. Willson
Summary: This study provides a description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey. The presence and abundance of specific bacterial and archaeal taxa indicate pollutant inputs and the study also observed microorganisms involved in the biodegradation of xenobiotics. The spatial occurrence of a specific degrader of persistent polychlorinated compounds is explained by sediment properties and contaminant concentrations.
MARINE POLLUTION BULLETIN
(2022)
Article
Biotechnology & Applied Microbiology
Shoichiro Kameoka, Daisuke Motooka, Satoshi Watanabe, Ryuichi Kubo, Nicolas Jung, Yuki Midorikawa, Natsuko O. Shinozaki, Yu Sawai, Aya K. Takeda, Shota Nakamura
Summary: The study compared 192 Japanese volunteers' fecal 16S analysis data using modified V1-V2 and standard V3-V4 primers. Results showed that the bacterial composition derived from the V34 region might differ from the actual abundance, suggesting that the modified V12 primer set is more desirable for analyzing the Japanese gut microbiota.
Article
Biotechnology & Applied Microbiology
Birgitte Moen, Solveig Langsrud, Ingunn Berget, Tove Maugesten, Trond Moretro
Summary: We report the bacterial composition in cleaning utensils and surface samples from 74 households across five European countries. Despite variations in kitchen practices and standards, a core microbiota was identified in European residential kitchens. Taxa associated with potential pathogens and fecal indicators were low in abundance but widely distributed throughout the households.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Immunology
Vitor Heidrich, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, Anamaria A. Camargo
Summary: Accessibility to next-generation sequencing (NGS) has enabled the profiling of microbial communities. Choosing the right 16S rRNA hypervariable region for sequencing is critical. This study evaluated the performance of different hypervariable regions in male urinary microbiota profiling and found that V1V2 region is more suitable.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
He Xu, Bijun Tian, Weihua Shi, Jing Tian, Xuexi Zhang, Jin Zeng, Man Qin
Summary: Tonsillar hypertrophy is a common disease in 3-to-6-year-old children, and there is a correlation between the oral microbiota and the healthy and hypertrophic states of tonsils.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Veterinary Sciences
Li Xi, Yumin Song, Xinxi Qin, Jincheng Han, Yung-Fu Chang
Summary: By comparing the gut microbial composition of healthy and diarrheic giraffes, this study found that diarrhea significantly impacts the diversity and composition of the gut microbiota by increasing the proportion of pathogenic bacteria and decreasing beneficial bacteria. It also identified specific changes in bacterial phyla and genera, providing insights for establishing prevention and treatment strategies for diarrhea in giraffes.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Patricia M. Oba, Meredith Q. Carroll, Kelly M. Sieja, Juliana P. de Souza Nogueira, Xiaojing Yang, Tammi Y. Epp, Christine M. Warzecha, Jessica L. Varney, Jason W. Fowler, Craig N. Coon, Kelly S. Swanson
Summary: The study aimed to investigate the fecal characteristics, microbiota, and metabolites of dogs fed a Saccharomyces cerevisiae fermentation product (SCFP) and subjected to exercise challenge in untrained and trained states. The results showed that exercise challenge reduced fecal pH and ammonia in all dogs and affected the fecal microbiota. SCFP did not significantly affect fecal characteristics or metabolites, but influenced the fecal Clostridium abundance. Exercise was found to be the primary cause of shifts in the fecal microbiota, with trained dogs experiencing more profound changes than untrained dogs.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Patricia M. Oba, Meredith Q. Carroll, Kelly M. Sieja, Xiaojing Yang, Tammi Y. Epp, Christine M. Warzecha, Jessica L. Varney, Jason W. Fowler, Craig N. Coon, Kelly S. Swanson
Summary: The study aimed to investigate the effect of Saccharomyces cerevisiae fermentation product (SCFP) supplementation on fecal characteristics, microbiota, and metabolites in dogs subjected to transport stress. The results showed that transport stress increased fecal indole concentrations and the relative abundances of certain bacteria, while decreasing the relative abundances of other bacteria. The interaction between diet and transport stress was significant, with SCFP supplementation affecting the relative abundances of different bacteria compared to the control group. The findings suggest that SCFP supplementation may provide benefits to dogs undergoing transport stress, but further research is needed to determine optimal dosages.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Immunology
Yanyan Que, Man Cao, Jianquan He, Qiang Zhang, Qiongyun Chen, Changsheng Yan, Aiqiang Lin, Luxi Yang, Zezhen Wu, Dan Zhu, Fengwu Chen, Zhangran Chen, Chuanxing Xiao, Kaijian Hou, Bangzhou Zhang
Summary: Research shows significant differences in microbial diversity between individuals with type 2 diabetes mellitus (T2DM) and controls, but not in microbial alpha diversity. Various operational taxonomic units (OTUs) and bacterial genera with significant odds ratios for T2DM were identified. The microbial characteristics of T2DM can be applied to other studies, improving detection accuracy and disease specificity for T2DM through training on multiple research studies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Marton Szoboszlay, Laetitia Schramm, David Pinzauti, Jeanesse Scerri, Anna Sandionigi, Manuele Biazzo
Summary: Nanopore sequencing is a promising technology for 16S rRNA gene amplicon sequencing, providing full-length reads at a low cost. Comparing with Illumina sequencing, Nanopore showed better accuracy, higher species-level taxonomic resolution, and better replicability. It is a better choice for studies focusing on species-level resolution, rare taxa investigation, and accurate estimation of richness.
Article
Medicine, Research & Experimental
Zhengrui Li, Rao Fu, Xufeng Huang, Xutao Wen, Ling Zhang
Summary: This study aimed to assess the correlation between oral microbiota and the extent of bone resorption in ORN patients. The results showed that the ORN group had higher microbial abundance and species diversity, and specific microbial communities were potentially associated with ORN. In addition, an imbalance in the oral microbiota may disrupt bone regeneration by regulating specific metabolic pathways that increase osteoclastic activity. Therefore, radiation-induced ORN is associated with significant changes in the oral microbiota.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Lois Rancilhac, Iker Irisarri, Claudio Angelini, Jan W. Arntzen, Wieslaw Babik, Franky Bossuyt, Sven Kuenzel, Tim Lueddecke, Frank Pasmans, Eugenia Sanchez, David Weisrock, Michael Veith, Ben Wielstra, Sebastian Steinfartz, Michael Hofreiter, Herve Philippe, Miguel Vences
Summary: Hybridization can lead to genealogical signatures in an organism's genome, causing challenges for phylogenetic inference methods. A phylotranscriptomic approach was used to study the evolutionary history of the Salamandridae and test for inter-lineage introgression. The study identified introgression events among different lineages and proposed hypotheses on the evolutionary relationships within the family.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Wengang Kang, Sten Anslan, Nicole Boerner, Anja Schwarz, Robin Schmidt, Sven Kuenzel, Patrick Rioual, Paula Echeverria-Galindo, Miguel Vences, Junbo Wang, Antje Schwalb
Summary: This study experimentally evaluated the effects of sediment sample quantity and bioinformatics pipelines on the metabarcoding data of diatoms, demonstrating minimal impact of sample quantity and high consistency among different bioinformatics pipelines. Taxonomic mismatches between metabarcoding and microscopy results were identified, potentially due to database incompleteness and taxonomic inconsistencies. Community analysis confirmed consistent results between microscopy and metabarcoding, highlighting the viability of metabarcoding in identifying diatom-environment relationships.
ECOLOGICAL INDICATORS
(2021)
Article
Multidisciplinary Sciences
Alejandro Ibanez, Molly C. Bletz, Galo Quezada, Robert Geffers, Michael Jarek, Miguel Vences, Sebastian Steinfartz
Summary: The diversity and richness of gut microorganisms in marine iguana populations are closely related to the genetic diversity of the host individuals, rather than being affected by El Nino-related nutrition deficiencies. During El Nino events, marine iguana populations face limited food resources, resulting in poor body condition, but with no significant differences in gut microbial structure.
Article
Multidisciplinary Sciences
Sebastian Kirchhof, Mariana L. Lyra, Ariel Rodriguez, Ivan Ineich, Johannes Mueller, Mark-Oliver Roedel, Jean-Francois Trape, Miguel Vences, Stephane Boissinot
Summary: Climate change greatly impacts the diversity and evolution of the world's biota. Research shows that the Old World lacertid lizard lineages diversified after the Eocene-Oligocene boundary, with a particular focus on the sub-Saharan Acanthodactylus species and their environmental adaptations.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Christophe Dufresnes, Alan Brelsford, Daniel L. Jeffries, Glib Mazepa, Tomasz Suchan, Daniele Canestrelli, Alfredo Nicieza, Luca Fumagalli, Sylvain Dubey, Inigo Martinez-Solano, Spartak N. Litvinchuk, Miguel Vences, Nicolas Perrin, Pierre-Andre Crochet
Summary: Research on frog and toad hybrid zones suggests that as lineages diverge, parts of the genome resist introgression, indicating that anuran speciation involves the gradual accumulation of multiple barrier loci scattered across the genome. This highly polygenic nature of reproductive isolation, along with the lack of hemizygous sex chromosomes, may explain the slower speciation clock in amphibians compared to other vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Barbara Santos, Molly C. Bletz, Joana Sabino-Pinto, Walter Cocca, Jean Francois Solofoniaina Fidy, Karen L. M. Freeman, Sven Kuenzel, Serge Ndriantsoa, Jean Noel, Tsanta Rakotonanahary, Miguel Vences, Angelica Crottini
Summary: The study found significant differences in the skin and gut bacterial communities between the invasive Asian common toad and a native frog in Madagascar, indicating a stable community across the toad's expansion but with richer and more diverse microbial communities.
Article
Fisheries
Douglas C. Woodhams, Joseph D. Madison, Molly C. Bletz, Julia McCartney, Brandon C. LaBumbard, Ross Whetstone, Nina B. McDonnell, Kathleen Preissler, Joana Sabino-Pinto, Jonah Piovia-Scott
Summary: The increasing study of emerging wildlife pathogens has raised concerns about laboratory escape and species spillover. Responsible self-regulation by research laboratories and institutional-level safeguards are important in mitigating pathogen transmission. Proactive biosecurity strategies, including annual laboratory risk assessments and comprehensive training for personnel, are critical to prevent disease spread and maintain public support for research on wildlife diseases.
DISEASES OF AQUATIC ORGANISMS
(2021)
Article
Ecology
Katharina C. Wollenberg Valero, Joan Garcia-Porta, Iker Irisarri, Lauric Feugere, Adam Bates, Sebastian Kirchhof, Olga Jovanovic Glavas, Panayiotis Pafilis, Sabrina F. Samuel, Johannes Mueller, Miguel Vences, Alexander P. Turner, Pedro Beltran-Alvarez, Kenneth B. Storey
Summary: Understanding the genetic basis of adaptation to different abiotic environments is crucial in the context of climate change. Through functional and comparative genomics, this study identified a set of genes in lacertid lizards and other vertebrates that are involved in physiological and morphological adaptations to climate. These genes form a tightly connected interactome enriched in functions related to adaptation to climate and organismal stress response.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sven Gippner, Scott L. Travers, Mark D. Scherz, Timothy J. Colston, Mariana L. Lyra, Ashwini Mohan, Malte Multzsch, Stuart Nielsen, Lois Rancilhac, Frank Glaw, Aaron M. Bauer, Miguel Vences
Summary: The dwarf geckos of the genus Lygodactylus are found in continental Africa, Madagascar, and South America. This study confirmed the monophyly of 14 Lygodactylus species groups and estimated the crown diversification of Lygodactylus to have started at 46 mya. Further research on related genera and phylogenomic approaches may help provide better biogeographic insights into the evolutionary history of these geckos.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Review
Veterinary Sciences
Laura Leiss, Anna Rauhaus, Andolalao Rakotoarison, Charles Fusari, Miguel Vences, Thomas Ziegler
Summary: The study explored the established ex situ populations for threatened Malagasy freshwater fish species, finding that there has been no significant improvement in ex situ conservation activities. It calls for better distribution of offspring, establishment of ex situ populations for species not yet kept in captivity, and the development of effective integrated in situ and ex situ conservation strategies.
Article
Multidisciplinary Sciences
Yu Wang, Hannah K. Smith, Evy Goossens, Lionel Hertzog, Molly C. Bletz, Dries Bonte, Kris Verheyen, Luc Lens, Miguel Vences, Frank Pasmans, An Martel
Summary: The research found that fire salamanders primarily feed on soft-bodied prey, with significant differences in diet composition between males and females, and higher gut microbiome diversity in males. Proximity to human activities may increase intestinal pathogen loads.
SCIENTIFIC REPORTS
(2021)
Article
Food Science & Technology
Mariana L. Lyra, Juliane P. C. Monteiro, Lois Rancilhac, Iker Irisarri, Sven Kuenzel, Eugenia Sanchez, Thais H. Condez, Omar Rojas-Padilla, Mirco Sole, Luis Felipe Toledo, Celio F. B. Haddad, Miguel Vences
Summary: The genus Brachycephalus, a group of miniature frogs from the Brazilian Atlantic Forest, consists of pumpkin-toadlets and flea-toads. The study using RNAseq data confirmed the existence of two separate pumpkin-toadlet clades, suggesting convergent evolution in morphology, coloration, and toxicity. Additionally, analysis of mitochondrial gene order revealed a new arrangement, with potential for Brachycephalus to become a model taxon for studying the evolution of coloration, body plan, and toxicity.
Article
Zoology
Quentin C. K. Hazard, Joana Sabino-Pinto, Adria Lopez-Baucells, Fabio Z. Farneda, Christoph F. J. Meyer, Ricardo Rocha
Summary: This study examined the reproductive phenology of nine bat species in Central Amazonia, with only three species exhibiting a bimodal reproductive pattern. Six species and the frugivore ensemble showed unimodal reproductive phenology, while gleaning animalivores displayed an amodal pregnancy pattern. The deviation from expected bimodal polyestry may be explained by a reproductive peak during the early wet season or local variation in the duration of the fruiting season.
Article
Multidisciplinary Sciences
Barbara Santos, Filipa M. S. Martins, Joana Sabino-Pinto, Fulvio Licata, Angelica Crottini
Summary: The microbiome of amphibian species is influenced by both water source and host identity, resulting in changes in microbial diversity and composition.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Vasiliki Mantzana-Oikonomaki, Martine Maan, Joana Sabino-Pinto
Summary: Accurate detection of wildlife pathogens is crucial for research and conservation efforts, and selecting the optimal DNA extraction method is key to improving detection efficiency and reducing project costs.
BIOLOGY METHODS & PROTOCOLS
(2021)