Article
Biotechnology & Applied Microbiology
Evan Mann, Shahrokh Shekarriz, Michael G. Surette
Summary: The intestinal lining is protected by a mucous barrier primarily composed of complex carbohydrates. Gut microbes use a variety of glycoside hydrolases to break down mucosal sugars, facilitating host colonization, but excessive breakdown may lead to barrier erosion, pathogen invasion, and inflammation. Sialidases from the microbiome, specifically the GH156 family, play a crucial role in human microbiomes, with potential therapeutic applications in cancer therapy. However, the full extent of GH156 sialidases and their functions in the human gut environment are still being explored.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Michael J. Tisza, Christopher B. Buck
Summary: Despite the challenges, this study reveals over 45,000 unique virus taxa sequences from thousands of datasets, with historically high per-genome completeness. By reanalyzing large publicly available case-control studies, over 2,200 strong virus-disease associations are found.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Shenghui Li, Ruochun Guo, Yue Zhang, Peng Li, Fang Chen, Xifan Wang, Jing Li, Zhuye Jie, Qingbo Lv, Hao Jin, Guangyang Wang, Qiulong Yan
Summary: This study analyzed the viral genomes in the human oral cavity and created the Oral Virus Database (OVD), which expands our knowledge of the phylogenetic diversity and host specificity of oral viruses. It also reveals differences in viral diversity and composition related to oral cavity habitats and host properties.
Article
Multidisciplinary Sciences
Shenghui Li, Ruochun Guo, Yue Zhang, Peng Li, Fang Chen, Xifan Wang, Jing Li, Zhuye Jie, Qingbo Lv, Hao Jin, Guangyang Wang, Qiulong Yan
Summary: The human oral cavity is an important reservoir for many unexplored viruses that play a crucial role in maintaining oral health and microbial balance. By analyzing a large dataset of oral metagenomes, the study reveals a wide range of diversity and host specificity in oral viruses, as well as variations in viral composition among different oral habitats.
Article
Microbiology
Daniel A. Schwartz, Josue A. Rodriguez-Ramos, Michael Shaffer, Rory M. Flynn, Rebecca A. Daly, Kelly C. Wrighton, Jay T. Lennon
Summary: Spore-forming bacteria are common in mammalian guts and affect host health and nutrition. Dormant spore production plays a crucial role in the colonization, persistence, and transmission of these bacteria. Recent studies have shown that phages can counteract dormancy-mediated defense mechanisms and alter the transitions between active and inactive states through the expression of phage-carried sporulation genes during infection. Identification of sporulation genes preferentially carried by phages that infect spore-forming bacteria can help in understanding the complex genetic network responsible for spore development.
Article
Genetics & Heredity
Chan Yeong Kim, Muyoung Lee, Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim, Insuk Lee
Summary: This study assembled 29,082 prokaryotic genomes from gut microbiomes of three under-represented Asian countries, forming an expanded catalog known as HRGM. The new 780 species identified were enriched in the Bacteroidaceae family, including those associated with high-fiber and seaweed-rich diets.
Article
Microbiology
Nicholas D. Youngblut, Jacobo De La Cuesta-Zuluaga, Ruth E. Ley
Summary: Tree-based diversity measures improve the identification of explanatory factors in microbial communities and provide unique insight into microbiome diversity partitioned by phenotype. They greatly improve machine learning model performance in predicting phenotype.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ruirui Hu, Rui Yao, Lei Li, Yueren Xu, Bingbing Lei, Guohao Tang, Haowei Liang, Yunjiao Lei, Cunyuan Li, Xiaoyue Li, Kaiping Liu, Limin Wang, Yunfeng Zhang, Yue Wang, Yuying Cui, Jihong Dai, Wei Ni, Ping Zhou, Baohua Yu, Shengwei Hu
Summary: The AnimalMetagenome DB integrates a large amount of metagenomic sequencing data from domestic and wild animals, making it easier for users to find data of interest and browse, search, and download the data.
Article
Gastroenterology & Hepatology
Shengzhi Yang, Zhenxin Fan, Jiawei Li, Xinqi Wang, Yue Lan, Bisong Yue, Miao He, Anyun Zhang, Jing Li
Summary: In this study, metagenome-assembled genomes (MAGs) were reconstructed from fecal samples of chronic diarrheal Rhesus macaques (RM) and asymptomatic individuals. Significant differences in microbial composition were observed between RM and human guts, and certain bacterial groups were found to be significantly reduced in chronic diarrhea RMs. These findings contribute to a better understanding of the diversity and function of RM gut microbiome.
Review
Gastroenterology & Hepatology
Kanchan Jaswal, Olivia A. Todd, Judith Behnsen
Summary: A diverse array of microorganisms, including bacteria as the most abundant and studied members, inhabit the human intestinal tract. However, the gut microbiome also consists of viruses, archaea, fungi, protists, and parasitic worms, which have been less studied but play important roles in health and disease. This review focuses on these understudied members, detailing their composition, development, and functional interactions with enteric pathogens. It presents both general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis, highlighting the need for including these communities in future gut microbiome research.
Article
Biochemical Research Methods
Brianna S. Chrisman, Kelley M. Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Peter Y. Washington, Christine Tataru, Shoko Iwai, Todd Z. DeSantis, Maude David, Dennis P. Wall
Summary: The study introduces a method of sequence-based biomarkers (SBBs) which groups and aggregates microbes using single variants and combinations of variants within their 16S sequences, performing on-par or better than existing methods in biomarker discovery and phenotype prediction.
BMC BIOINFORMATICS
(2021)
Article
Evolutionary Biology
William R. Shoemaker, Daisy Chen, Nandita R. Garud
Summary: Genetic variation in the human gut microbiome plays a crucial role in various phenotypes. However, our understanding of its origins and maintenance is limited. By comparing evolutionary processes across different species, we can identify universal trends and deviations. The human gut microbiome offers unparalleled potential for comparative population genomics studies.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Kristopher Kieft, Karthik Anantharaman
Summary: Temperate phages (prophages) are dormant components of host cells before activating and lysing the host. It is challenging to identify if a prophage has activated. In this study, researchers developed an automated software tool called PropagAtE to estimate the lytic or lysogenic stage of prophage infection. Application of PropagAtE to various environments revealed distinct activation signatures of prophages and identified active prophage populations correlated with specific treatment groups.
Article
Biochemistry & Molecular Biology
Francisco Zorrilla, Filip Buric, Kiran R. Patil, Aleksej Zelezniak
Summary: The metaGEM pipeline enables metabolic modeling of multi-species communities directly from metagenomes, showcasing fully represented metabolism in GEMs reconstructed from metagenomes and capturing intraspecies metabolic diversity. It provides a resource of metabolic models and showcases community-level modeling of microbiomes associated with disease conditions, allowing the generation of mechanistic hypotheses.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Masato Kogawa, Yohei Nishikawa, Tatsuya Saeki, Takuya Yoda, Koji Arikawa, Haruko Takeyama, Masahito Hosokawa
Summary: Single-cell genomics is a promising approach for studying uncultured bacteria. In this study, a single-cell amplified genome long-read assembly (scALA) workflow was developed to construct complete circular single-amplified bacterial genomes. Through scALA, 16 complete circular genomes of specific bacteria were obtained from human fecal samples, providing insights into microbial evolution, adaptation to environmental changes, and interactions with hosts.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
James W. Marsh, Ruth E. Ley
Article
Microbiology
Nicholas D. Youngblut, Jacobo De La Cuesta-Zuluaga, Ruth E. Ley
Summary: Tree-based diversity measures improve the identification of explanatory factors in microbial communities and provide unique insight into microbiome diversity partitioned by phenotype. They greatly improve machine learning model performance in predicting phenotype.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Taichi A. Suzuki, Ruth E. Ley
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Hagay Enav, Fredrik Baeckhed, Ruth E. Ley
Summary: The colonization of the infant microbiome is a complex process influenced by ecological forces and environmental conditions. Recent advancements in strain-level analysis have revealed the immense complexity of the system, providing a better understanding of how strains of the same species spread, colonize, evolve, and impact the host.
CELL HOST & MICROBE
(2022)
Article
Gastroenterology & Hepatology
Benoit Chassaing, Charlene Compher, Brittaney Bonhomme, Qing Liu, Yuan Tian, William Walters, Lisa Nessel, Clara Delaroque, Fuhua Hao, Victoria Gershuni, Lillian Chau, Josephine Ni, Meenakshi Bewtra, Lindsey Albenberg, Alexis Bretin, Liam McKeever, Ruth E. Ley, Andrew D. Patterson, Gary D. Wu, Andrew T. Gewirtz, James D. Lewis
Summary: In healthy adults, consumption of the synthetic emulsifier CMC was found to exacerbate postprandial abdominal discomfort, disrupt gut microbiota and metabolome composition, leading to reduced diversity, and possibly contributing to the development of chronic inflammatory diseases.
Article
Microbiology
Samuel E. Barnett, Nicholas D. Youngblut, Daniel H. Buckley
Summary: Soil dwelling microorganisms play a crucial role in the carbon cycle by both degrading and stabilizing soil organic matter. However, the factors that drive the variation in bacterial community structure and function with respect to land use are still poorly understood. In this study, a multi-substrate DNA stable isotope probing experiment was conducted to examine the dynamics of bacterial growth and carbon assimilation in different land-use habitats. The results showed that carbon mineralization, community composition, and carbon assimilation dynamics all varied with land use. Furthermore, microbial community dynamics were found to influence carbon assimilation dynamics and were associated with soil DNA content. The findings suggest that soil DNA yield, which is easily measurable, may be a useful indicator for predicting microbial community dynamics related to soil carbon cycling.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Yishay Pinto, Sigal Frishman, Sondra Turjeman, Adi Eshel, Meital Nuriel-Ohayon, Oshrit Shrossel, Oren Ziv, William Walters, Julie Parsonnet, Catherine Ley, Elizabeth L. Johnson, Krithika Kumar, Ron Schweitzer, Soliman Khatib, Faiga Magzal, Efrat Muller, Snait Tamir, Kinneret Tenenbaum-Gavish, Samuli Rautava, Seppo Salminen, Erika Isolauri, Or Yariv, Yoav Peled, Eran Poran, Joseph Pardo, Rony Chen, Moshe Hod, Elhanan Borenstein, Ruth E. Ley, Betty Schwartz, Yoram Louzoun, Eran Hadar, Omry Koren
Summary: This study comprehensively analyzed the gut microbiome, metabolome, inflammatory cytokines, nutrition, and clinical records of 394 women during the first trimester of pregnancy in order to predict the onset of gestational diabetes mellitus (GDM) earlier than currently accepted. The study also demonstrated the role of the gut microbiome in the development of GDM. These findings provide potential targets for early diagnostics and therapeutic intervention in the prevention of GDM.
Article
Immunology
Sara J. Clasen, Michael E. W. Bell, Andrea Borbon, Du-Hwa Lee, Zachariah M. Henseler, Jacobo de la Cuesta-zuluaga, Katarzyna Parys, Jun Zou, Yanling Wang, Veronika Altmannova, Nicholas D. Youngblut, John R. Weir, Andrew T. Gewirtz, Youssef Belkhadir, Ruth E. Ley
Summary: Flagellin, the protein subunit of bacterial flagellum, can either stimulate or evade the innate immune receptor Toll-like receptor 5 (TLR5) through pattern recognition. Weak agonism of flagellins from commensal bacteria brings up the question of how TLR5 response is tuned. This study discovered a class of flagellin-TLR5 interaction called silent recognition, which enables flagellin binding to preformed TLR5 dimers and significantly increases TLR5 signaling.
SCIENCE IMMUNOLOGY
(2023)
Article
Microbiology
William A. Walters, Andrea C. Granados, Catherine Ley, Scot Federman, Doug Stryke, Yale Santos, Thomas Haggerty, Alicia Sotomayor-Gonzalez, Venice Servellita, Ruth E. Ley, Julie Parsonnet, Charles Y. Chiu
Summary: The human gut virome and its early life development are not well understood. This study used viral metagenomic sequencing to examine the virome composition of infants and their mothers longitudinally. It was found that the infant virome primarily consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, while the maternal virome had a larger presence of undetected vertebrate viruses. The development of the infant virome was mainly influenced by dietary, infectious, and environmental factors rather than direct maternal acquisition.
CELL HOST & MICROBE
(2023)
Article
Biochemical Research Methods
Olga Mineeva, Daniel Danciu, Bernhard Schoelkopf, Ruth E. Ley, Gunnar Ratsch, Nicholas D. Youngblut
Summary: The number of published metagenome assemblies is increasing rapidly. To address the challenge of detecting misassemblies in taxonomically novel genomic data, a deep learning approach called ResMiCo was developed. ResMiCo was shown to be more accurate than existing methods and robust to novel taxonomic diversity and assembly methods. The tool can be used for quality control and optimization of metagenome assemblies.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Jacobo de la Cuesta-zuluaga, Kelsey E. Huus, Nicholas D. Youngblut, Juan S. Escobar, Ruth E. Ley
Summary: Obesity and cardiometabolic disease are associated with changes in the gut microbiome. Through studying a cohort of 408 adults from Colombia, researchers validated previously reported features of the gut microbiome function and diversity correlated with obesity or poor cardiometabolic health status. The results showed that obesity, rather than metabolic status, is the main driver of differences in gut microbiome functions and structure in individuals with or without poor cardiometabolic health.
Article
Biochemical Research Methods
Patrick Mueller, Jacobo de la Cuesta-Zuluaga, Michael Kuhn, Maral Baghai Arassi, Tim Treis, Sonja Blasche, Michael Zimmermann, Peer Bork, Kiran Raosaheb Patil, Athanasios Typas, Sarela Garcia-Santamarina, Lisa Maier
Summary: The human gut microbiome plays a vital role in health, and disturbances in its composition are associated with various diseases. Small-molecule xenobiotics, such as drugs and chemical pollutants, can alter the gut microbiota and are recognized as one of the main factors affecting microbiome diversity. This article presents a high-throughput screening protocol that allows for the investigation of the inhibitory effects of hundreds of xenobiotics on anaerobic gut bacteria. The authors have developed an experimental setup and protocol that enables the testing of up to 5,000 compounds on a target gut species within 5 days under strict anaerobic conditions. The protocol can also be modified to test the effects of drugs on microbial communities obtained from stool samples. This protocol is expected to accelerate the study of interactions between small molecules and the gut microbiome, providing a deeper understanding of this microbial ecosystem and its relationship to human health.