Article
Engineering, Environmental
Vicente Gomez-Alvarez, Sallamaari Siponen, Ari Kauppinen, Anna-Maria Hokajarvi, Ananda Tiwari, Anniina Sarekoski, Ilkka T. Miettinen, Eila Torvinen, Tarja Pitkanen
Summary: The study used next-generation sequencing technologies to analyze the water microbiome in five waterworks in Finland. The presence and type of disinfectant residual exert selective pressure on the microbial community. The microbial community in non-disinfected drinking water systems is important and maintaining disinfectant residual is crucial for reducing microbial numbers and diversity.
Review
Microbiology
Tae Woong Whon, Na-Ri Shin, Joon Yong Kim, Seong Woon Roh
Summary: Recent advances in environmental microbial genomics have improved our understanding of the interactions between microbial communities and their niche in the host gut; integration of various omics data to study the gut microbiome has become increasingly common, although downstream analysis and interpretation of complex omics data remain challenging. Studies have explored gut microbiome characteristics using omics approaches, and recent discussions have focused on analytics programs and advanced techniques for further utilization of omics data.
JOURNAL OF MICROBIOLOGY
(2021)
Article
Microbiology
Joshua C. Gil, Sarah M. Hird
Summary: This study investigated the accuracy of simulated metagenomes in a nonmodel system, the Canada goose, and revealed some unique functional characteristics of the microbiome in this nonmodel organism. It also highlighted the limitations of simulated metagenomes in specific gene prediction.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Xiaochun Shi, Bei Gao, Anvesha Srivastava, Zahra Izzi, Yoosif Abdalla, Weishou Shen, Dominic Raj
Summary: Alterations in gut microbiota in hemodialysis patients contribute to uremic toxicity and immune dysregulation, leading to higher infection risk and mortality. The study found significant changes in microbial species, metabolic pathways, antibiotic resistance, and virulence factors in hemodialysis patients compared to controls, indicating the importance of understanding virulence factors in predisposing HD patients to infection and developing targeted treatment strategies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Oncology
Paul Vinu Salachan, Karina Dalsgaard Sorensen
Summary: The role of microbiota in human health and disease, including cancer types, is established, but its specific role in prostate cancer development, progression, and treatment response is less understood. The lack of better risk stratification tools may be due to gaps in knowledge regarding bacterial infections and inflammation signatures as risk factors. Further research is needed to find the biological link between microbiome and prostate carcinogenesis.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Michael T. France, Li Fu, Lindsay Rutt, Hongqiu Yang, Michael S. Humphrys, Shilpa Narina, Pawel M. Gajer, Bing Ma, Larry J. Forney, Jacques Ravel
Summary: This study characterized the genetic composition and transcriptional activities of vaginal microbiota in healthy women to determine the factors that drive vaginal community composition. The results show that species abundance does not always indicate its transcriptional activity and impending changes in community composition can be predicted from metatranscriptomic data. Additionally, the degradation of mucin by communities not dominated by Lactobacillus may play a role in their association with adverse health outcomes. The transcriptional activities of L. crispatus, L. iners, and Gardnerella vaginalis vary with the taxonomic composition of the communities in which they reside.
Article
Multidisciplinary Sciences
Rachel Gilroy, Anuradha Ravi, Maria Getino, Isabella Pursley, Daniel L. Horton, Nabil-Fareed Alikhan, Dave Baker, Karim Gharbi, Neil Hall, Mick Watson, Evelien M. Adriaenssens, Ebenezer Foster-Nyarko, Sheikh Jarju, Arss Secka, Martin Antonio, Aharon Oren, Roy R. Chaudhuri, Roberto La Ragione, Falk Hildebrand, Mark J. Pallen
Summary: This study provides new insights into the taxonomic diversity of the chicken gut microbiome through metagenomic and culture-based analyses. It identified hundreds of novel candidate bacterial genera and species, proposed a scalable nomenclature system, and cultured and sequenced novel bacterial species from chicken feces. The findings expand the known diversity of the chicken gut microbiome and serve as a valuable resource for future studies in this field.
Article
Gastroenterology & Hepatology
Juan P. Molina Ortiz, Mark Norman Read, Dale David McClure, Andrew Holmes, Fariba Dehghani, Erin Rose Shanahan
Summary: This study used genomic reconstruction modeling to infer the metabolic attributes and nutritional requirements of 816 gut strains, focusing on vitamin exchanges at different levels of community organization. The results showed that only 91 strains could satisfy their vitamin requirements, while the rest showed various degrees of dependence on external sources. The study also revealed marked metabolic differences in human gut microbial community enterotype indicators. Additionally, pre-defined interaction modules of gut species driven by, or independent of vitamin exchanges were identified.
Article
Biochemistry & Molecular Biology
Tatiana A. Gurbich, Alexandre Almeida, Martin Beracochea, Tony Burdett, Josephine Burgin, Guy Cochrane, Shriya Raj, Lorna Richardson, Alexander B. Rogers, Ekaterina Sakharova, Gustavo A. Salazar, Robert D. Finn
Summary: An increasing number of shotgun metagenomic datasets now yield metagenome-assembled genomes (MAGs), but the lack of standardization in their generation, annotation, and storage hinders the discovery and comparison of MAG collections. To address this, MGnify Genomes offers a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Users can access visualized species representative sequences and annotations on the MGnify website and download the full catalogue and associated analysis outputs from MGnify servers. Currently, there are seven available biomes with over 300,000 genomes representing 11,048 non-redundant species and including 36 taxonomic classes not represented by cultured genomes. MGnify Genomes is accessible at https://www.ebi.ac.uk/metagenomics/browse/genomes/.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jie Zheng, Elizabeth Reed, Padmini Ramachandran, Andrea Ottesen, Eric W. Brown, Yu Wang
Summary: This study characterized the function and taxonomy of actively transcribed genes in sprout spent irrigation water (SSIW) from Salmonella-contaminated alfalfa seeds. Results showed changes in the microbiome structure and gene expression patterns related to sprouting in response to Salmonella contamination. These findings enhance our understanding of the interaction between Salmonella and the sprout microbiome.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Oxana M. Drapkina, German A. Ashniev, Olga A. Zlobovskaya, Adel A. Yafarova, Elena Dementeva, Anastasia N. Kaburova, Ivan O. Meshkov, Anna F. Sheptulina, Anton R. Kiselev, Anna Kontsevaya, Linar M. Zhamalov, Sergey N. Koretskiy, Mariya S. Pokrovskaya, Alexandra Akinshina, Anjelica Zagaynova, Mariia Lukashina, Andrey Kirillov, Ivan A. Abramov, Larisa R. Tolkacheva, Irina O. Bikaeva, Evgeniya Glazunova, German A. Shipulin, Maria M. Bobrova, Valentin V. Makarov, Anton A. Keskinov, Vladimir S. Yudin, Sergey M. Yudin
Summary: To further understand the pathogenesis of cardiovascular disease, this study explored the role of gut microbiota in atherosclerotic cardiovascular disease and heart failure, using multiple evaluation methods. The results showed some differences in microbiota composition between different disease groups and the control group, expanding the knowledge on the correlation between gut microbiota and cardiovascular diseases.
Article
Veterinary Sciences
Agata Jozefiak, Mateusz Rawski, Bartosz Kieronczyk, Damian Jozefiak, Jan Mazurkiewicz
Summary: This study evaluated the effects of two diets containing mealworm and superworm on the gut microbiome of sea trout fingerlings. The results showed that both insect meals did not have a significant impact on the growth and survival rate of sea trout. However, there were noticeable microbiome differences at lower taxonomic levels, particularly with the superworm meal.
BMC VETERINARY RESEARCH
(2023)
Article
Microbiology
Alexander G. Shaw, Kathleen Sim, Graham Rose, David J. Wooldridge, Ming-Shi Li, Raju Misra, Saheer Gharbia, J. Simon Kroll
Summary: The study identified two distinct microbial community patterns in infants with necrotising enterocolitis (NEC): one with low levels of CpG DNA and another with high abundances of LPS-expressing organisms. These patterns may represent extremes of TLR4 pathway stimulation.
Article
Environmental Sciences
Weronika Goraj, Anna Pytlak, Beata Kowalska, Dariusz Kowalski, Jaroslaw Grzadziel, Anna Szafranek-Nakonieczna, Anna Galazka, Zofia Stepniewska, Witold Stepniewski
Summary: The study revealed that the construction material strongly influences the microbiome composition, with plastic pipes creating a more convenient environment for potentially pathogenic taxa compared to cast iron. Additionally, biofilms were described as complex habitats with sharp oxidation-reduction gradients, and DWDS proved to be a useful tool for studying the ecology of rare bacterial phyla.
ENVIRONMENTAL RESEARCH
(2021)
Article
Microbiology
Mary Maranga, Pawel Szczerbiak, Valentyn Bezshapkin, Vladimir Gligorijevic, Chris Chandler, Richard Bonneau, Ramnik J. Xavier, Tommi Vatanen, Tomasz Kosciolek
Summary: In the past decade, there has been rapid accumulation of genomic data from microbial communities due to advancements in high-throughput sequencing technologies. However, the majority of microbial gene functions remain uncharacterized. To address this, a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations (DeepFRI) has been developed. This workflow significantly improves the annotation coverage and allows for the analysis of the functional potential of individual bacterial species, leading to a better understanding of the human gut microbiome in health and disease.
Article
Toxicology
Janneke Elzinga, Menno Grouls, Guido J. E. J. Hooiveld, Meike van der Zande, Hauke Smidt, Hans Bouwmeester
Summary: There is a need for standardized in vitro models of the human intestinal tract to study intestinal health without using animals. The Caco-2 cell line is a widely accepted and characterized model for studying intestinal drug transport, host-microbe interactions, and toxicity. We investigated the effect of different experimental variables on gene expression using transcriptome analysis of Caco-2 cells grown on permeable membranes. Our analysis revealed a weak association between experimental variables and gene expression, possibly due to heterogeneity in cell culture practice and inadequate reporting. This highlights the need for improved reporting protocols and serves as a template for future comparative studies.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Fisheries
Pacharaporn Angthong, Tanaporn Uengwetwanit, Umaporn Uawisetwathana, Jasper J. Koehorst, Sopacha Arayamethakorn, Peter J. Schaap, Vitor Martins Dos Santos, Metavee Phromson, Nitsara Karoonuthaisiri, Sage Chaiyapechara, Wanilada Rungrassamee
Summary: To understand the interaction between shrimp and intestinal microbiota, multidisciplinary platforms were used to analyze the metagenome, transcriptome, and metabolome. The study found that exposure to Vibrio harveyi disrupted the bacterial communities in the shrimp intestine. Gene expression analysis revealed upregulation of immune-related pathways, while metabolomics analysis showed changes in lipid metabolism. The findings suggest the importance of lipid metabolism and the impact of pathogenic Vibrio on shrimp immunity. This study provides valuable insights into the host-gut microbial relationship and its influence on shrimp innate immunity.
Article
Agricultural Engineering
M. Atasoy, W. T. Scott Jr., K. van Gijn, J. J. Koehorst, H. Smidt, A. A. M. Langenhoff
Summary: Optimizing bioreactor performance is crucial for sustainable and energy-efficient removal of micropollutants in tertiary treatment. The resident microbial community plays a significant role in bioreactor performance, hence a deeper understanding of community dynamics is essential. By characterizing the microbial communities in three different bioreactors used for organic matter removal, an interdependency between bioreactor performance and microbial community profile was observed. A generalized Lotka-Volterra model was established to understand the interactions in the microbial community and develop strategies for improving bioreactor performance.
BIORESOURCE TECHNOLOGY
(2023)
Article
Psychology, Developmental
Yangwenshan Ou, Clara Belzer, Hauke Smidt, Carolina de Weerth
Summary: The study investigated the development of gut microbiota in children during the first 14 years of life and its relation to mental health problems in puberty. The analysis of fecal microbiota composition revealed the presence of four distinct microbial clusters in puberty. Prevotella 9 and Faecalibacterium were found to be associated with externalizing behavior and social anxiety, respectively. Further studies are needed to validate these findings and explore the underlying mechanisms.
EUROPEAN CHILD & ADOLESCENT PSYCHIATRY
(2023)
Review
Pediatrics
Desiree F. Baaleman, Carrie A. M. Wegh, Tessa J. M. de Leeuw, Faridi S. van Etten-Jamaludin, Elaine E. Vaughan, Margriet H. C. Schoterman, Clara Belzer, Hauke Smidt, Merit M. Tabbers, Marc A. Benninga, Ilan J. N. Koppen
Summary: A systematic review was conducted to estimate normal reference values for defecation frequency and stool consistency in healthy children up to age 4. The results showed that younger infants have a higher frequency of defecation compared to young children, and the type of feeding and age also have an impact on defecation frequency and stool consistency.
JOURNAL OF PEDIATRICS
(2023)
Article
Microbiology
Thanaporn Laothanachareon, Enrique Asin-Garcia, Rita J. M. Volkers, Juan Antonio Tamayo-Ramos, Vitor A. P. Martins dos Santos, Peter J. Schaap
Summary: Aspergillus niger is a powerful microbial cell factory for producing organic acids. The regulation of the glucose oxidase (Gox) expression system, which is involved in gluconic acid biosynthesis, has been recently discovered. The study found that hydrogen peroxide plays a crucial role as a signaling molecule in inducing this system. The facilitated diffusion of hydrogen peroxide via aquaporin water channels (AQPs) was studied in this research.
Article
Biotechnology & Applied Microbiology
Andrea Aldas-Vargas, Jannigje G. G. Kers, Hauke Smidt, Huub H. M. Rijnaarts, Nora B. B. Sutton
Summary: Groundwater in The Netherlands is the main source of drinking water, but pesticide presence threatens its quality. Biodegradation is a natural process that can help remove pesticides. However, the oligotrophic groundwater conditions may limit biodegradation due to the lack of microbial communities capable of degrading pesticides. In this study, bioaugmentation with enriched mixed inocula was used to enhance pesticide biodegradation, and the effect of different redox conditions on biodegradation was observed.
Article
Ecology
Asimenia Gavriilidou, Burak Avci, Anastasia Galani, Michelle A. Schorn, Colin J. Ingham, Thijs J. G. Ettema, Hauke Smidt, Detmer Sipkema
Summary: Using genome-centric metagenomics, researchers revealed the phylogenomic placement of the candidate phylum Dadabacteria and predicted the metabolism of sponge-associated members. The results showed that these strains are aerobic heterotrophs capable of synthesizing amino acids, vitamins and cofactors, degrading complex carbohydrates, and exhibiting host-specific gene adaptations. Additionally, fluorescence in situ hybridization revealed the morphology and lifestyle of a member of Ca. Desulfobacterota.
Review
Microbiology
Angela Sessitsch, Steve Wakelin, Michael Schloter, Emmanuelle Maguin, Tomislav Cernava, Marie-Christine Champomier-Verges, Trevor C. Charles, Paul D. Cotter, Ilario Ferrocino, Aicha Kriaa, Pedro Lebre, Don Cowan, Lene Lange, Seghal Kiran, Lidia Markiewicz, Annelein Meisner, Marta Olivares, Inga Sarand, Bettina Schelkle, Joseph Selvin, Hauke Smidt, Leo van Overbeek, Gabriele Berg, Luca Cocolin, Yolanda Sanz, Wilson Lemos Fernandes, S. J. Liu, Matthew Ryan, Brajesh Singh, Tanja Kostic
Summary: Microbiomes play crucial roles in ecosystem functioning, supporting planetary health through nutrient cycling, climate regulation, and water filtration. They are closely associated with complex multicellular organisms and contribute to the health of their hosts. However, there is still limited understanding of microbiome transfer and connectivity.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Biochemical Research Methods
William T. R. Scott Jr, Sara Benito-Vaquerizo, Johannes R. Zimmermann, Djordje Bajic, Almut R. Heinken, Maria Suarez-Diez, Peter R. Schaap
Summary: This study examined and evaluated 24 constraint-based modeling tools for genome-scale metabolic modeling of microbial consortia. It found that newer, more accessible, and well-documented tools generally outperformed older tools, but some older tools had tradeoffs in terms of accuracy or flexibility. The study provides recommendations for researchers in choosing the most suitable tools and opportunities for improvement in metabolic modeling of multi-species microbial consortia.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Bart Nijsse, Peter J. Schaap, Jasper J. Koehorst
Summary: The life sciences are a major source of scientific data. Reusing and connecting these data can lead to new concepts and insights. However, the availability of easy-to-adopt implementations that fulfill the needs of data producers is limited. In response, the FAIR Data Station, a lightweight application written in Java, has been developed to support researchers in managing research metadata according to the FAIR principles. It includes modules for generating metadata templates, validating recorded values, and converting metadata into RDF format.
Article
Microbiology
Caifang Wen, Mirelle Geervliet, Hugo de Vries, Lluis Faba, Petra J. Roubos-van den Hil, Kerstin Skovgaard, Huub F. J. Savelkoul, Henk A. Schols, Jerry M. Wells, Edwin Tijhaar, Hauke Smidt
Summary: The study found that adding a fermented feed additive - rye overgrown with mycelium of Agaricus subrufescens can modulate gut microbiota and immune system development in pigs. This supplementation may contribute to improving the health of piglets during the weaning transition period and reducing the use of antibiotics.
Article
Environmental Sciences
Sara N. Jimenez-Volkerink, Maria Jordan, Hauke Smidt, Cristina Minguillon, Joaquim Vila, Magdalena Grifoll
Summary: By studying a specific microbial consortium in PAH-contaminated soils, it was discovered that the degradation of the carcinogenic compound BaAQ may occur through the Baeyer-Villiger monooxygenase (BVMOs) pathway, and that horizontal gene transfer may play a significant role in this degradation process.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Correction
Biology
Andra Waagmeester, Egon L. Willighagen, Andrew I. Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernandez-Alvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
Article
Gastroenterology & Hepatology
Yangwenshan Ou, Eline Rots, Clara Belzer, Hauke Smidt, Carolina de Weerth
Summary: An increasing number of studies have shown the connection between gut microbiota and mental health. This study investigated the composition of gut microbiota in low-risk children during early puberty, and explored the behavioral associations with gut microbiota composition and metabolites. The study also explored the potential role of sex in these associations.