Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Review
Cell Biology
Heloise Tudela, Sandrine P. Claus, Maya Saleh
Summary: The gut microbiota, a diverse community of microorganisms in the gastrointestinal tract, has a significant impact on health and disease. Keystone species, essential microbes for microbiota balance, play crucial roles in maintaining essential functions and their identification is crucial for the development of microbiome-based therapeutics. Understanding the functions of keystone species is a major step towards comprehending microbiome dynamics in disease.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Environmental Sciences
Hannah E. Laue, Yuka Moroishi, Thomas J. Palys, Brian P. Jackson, Juliette C. Madan, Margaret R. Karagas
Summary: Gut bacteria are associated with the impact of environmental exposures on human systems. The study found a correlation between arsenic-metabolizing bacteria in the infant gut microbiome and urinary arsenic excretion. Some arsenic-related gene pathways were associated with arsenic exposure and speciation, with stronger associations observed in infants delivered by caesarean section.
ENVIRONMENTAL RESEARCH
(2022)
Review
Immunology
Michele Zuppi, Heather L. Hendrickson, Justin M. O'Sullivan, Tommi Vatanen
Summary: Phages are viruses that infect bacteria and are widely found in various environments. They are abundant in the human gut and may play an important role in modulating the gut ecosystem. Although the extent of their influence on the gut ecosystem is not fully understood, there is increasing evidence supporting their significance in the gut microbiome.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Connie A. Rojas, Kay E. Holekamp, Mariette Viladomat Jasso, Valeria Souza, Jonathan A. Eisen, Kevin R. Theis
Summary: This study investigated the variability and function of gut microbiome in wild spotted hyenas over a 23-year period and found that the composition and function of the microbiome are influenced by host factors such as age and diet. The study also discovered novel genomic diversity in the hyena gut microbiome.
Review
Immunology
Ziyi Zhang, Zhihui Liu, Ao Lv, Chenhui Fan
Summary: Recently, researchers have discovered a possible link between Parkinson's disease and the gut microbiome, establishing the microbiome-gut-brain axis. Toll-like receptor 2 (TLR2) and Toll-like receptor 4 (TLR4) have been identified as key players in maintaining gut homeostasis. Dysregulation of TLR2 and TLR4 is observed in Parkinson's disease patients, suggesting their involvement in early gut dysfunction. This study reviews clinical, animal, and in vitro studies to investigate the role of TLR2 and TLR4 dysfunction in Parkinson's disease, and proposes a conceptual model where microbial dysbiosis disrupts the gut barrier and TLR2/TLR4 signaling, leading to chronic gut dysfunction and α-synuclein aggregation.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Eric Banan-Mwine Daliri, Fred Kwame Ofosu, Ramachandran Chelliah, Byong H. Lee, Deog-Hwan Oh
Summary: The application of multi-omic technologies in gut microbiome studies has unveiled the comprehensive interaction between commensals in health and disease. However, challenges remain in identifying the origin and function of certain proteins and metabolites in gut samples, which may be overcome by combining different omics techniques. Future perspectives in this area include overcoming challenges and advancing our understanding of the gut microbiome through the integration of various omic approaches.
Article
Medicine, General & Internal
Joonatan Palmu, Christin S. Boerschel, Alfredo Ortega-Alonso, Lajos Marko, Michael Inouye, Pekka Jousilahti, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Friederike Gutmann, Dominik Linz, Veikko Salomaa, Aki S. Havulinna, Sofia K. Forslund, Rob Knight, Leo Lahti, Teemu Niiranen, Renate B. Schnabel
Summary: This study found that the gut microbiome composition is associated with the risk of atrial fibrillation (AF). Certain microbial genera were found to be related to the occurrence and prediction of AF. These findings establish the basis for using microbiome profiling in predicting AF risk, but further research is needed before microbiome sequencing can be used in prevention and targeted treatment of AF.
Article
Allergy
Yang Liu, Shu Mei Teo, Guillaume Meric, Howard H. F. Tang, Qiyun Zhu, Jon G. Sanders, Yoshiki Vazquez-Baeza, Karin Verspoor, Ville A. Vartiainen, Pekka Jousilahti, Leo Lahti, Teemu Niiranen, Aki S. Havulinna, Rob Knight, Veikko Salomaa, Michael Inouye
Summary: This study found significant associations between gut microbiome and incident asthma and COPD in a population-based cohort of 7115 adults. Machine learning models demonstrated the predictive capabilities of baseline gut microbiome abundance for asthma and COPD, outperforming individual conventional risk factors. The integration of gut microbiome and conventional risk factors further improved prediction capacities.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Article
Microbiology
Maia Segura-Wang, Nikolaus Grabner, Andreas Koestelbauer, Viviana Klose, Mahdi Ghanbari
Summary: Increasing evidence suggests that chicken gastrointestinal microbiota plays a crucial role in metabolic functions and is associated with economic parameters. This study utilized metagenomic assembled genomes (MAGs) from chicken GIT samples to better understand the metabolic potential at different ages. Results showed age-dependent shifts in the abundance of genes involved in carbohydrate digestion and SCFA production, highlighting the importance of specific enzyme families in the microbial community.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Gabrielle Potocki-Veronese
Summary: Transport is a crucial step in the metabolism of glycosides by bacteria, which is key for microbiota function and equilibrium. However, our understanding of how bacteria utilize glycosides is limited by the lack of knowledge about transport proteins. In this study, an activity-based screening method was used to identify functional glycoside transporters from microbiomes. The results provide new insights into how glycosides are selectively metabolized by bacteria and offer a new approach to screening for glycoside-transporter specificity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
James F. Colbert, Joshua M. Kirsch, Christopher L. Erzen, Christophe J. Langouet-Astrie, Grace E. Thompson, Sarah A. McMurtry, Jennifer M. Kofonow, Charles E. Robertson, Elizabeth J. Kovacs, Ryan C. Sullivan, Joseph A. Hippensteel, Namrata V. Sawant, Nicole J. De Nisco, Bruce D. McCollister, Robert S. Schwartz, Alexander R. Horswill, Daniel N. Frank, Breck A. Duerkop, Eric P. Schmidt
Summary: Previous research has focused on the impact of host factors on sepsis outcomes in older adults but failed to find effective therapies. This study suggests that the increased susceptibility of the elderly to sepsis is not only due to host factors but also changes in the virulence of gut bacteria. The research shows that although the composition of bacterial communities in the gut changes subtly with age, there is an overabundance of genomic virulence factors that affect host immune evasion.
Article
Endocrinology & Metabolism
Jiachong Liang, Sikandar Ali, Chunrong Lv, Hongyuan Yang, Xiaoqi Zhao, Xiaojun Ni, Chunyan Li, Baiji Danzeng, Yajing Wang, Guobo Quan
Summary: In this study, 16S rDNA sequencing and metagenomic strategy were used to identify fecal bacteria in lactating ewes fed with different levels of dietary proteins. The results showed that the levels of dietary proteins had a significant impact on the populations and genes of fecal bacteria. This study could contribute to the development of a dietary formula for lactating ewes to optimize their growth and health.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Medicine, Research & Experimental
Yaneth Citlalli Orbe-Orihuela, Elizabeth Ernestina Godoy-Lozano, Alfredo Lagunas-Martinez, Ana Cristina Castaneda-Marquez, Sofia Murga-Garrido, Cinthya Estefhany Diaz-Benitez, Adrian Ochoa-Leyva, Fernanda Cornejo-Granados, Miguel Cruz, Karel Estrada, Victor Hugo Bermudez-Morales, Alejandro Sanchez-Flores, AnaIsabel Burguete-Garcia
Summary: This study aimed to evaluate the taxonomic profile of gut microbiota using metagenomics and its association with diet-dependent childhood obesity. The results showed that children with an abundance of Holdemania spp. and high protein and complex carbohydrate consumption had lower z-BMI, waist circumference, and hip circumference. In contrast, Coprococcus catus showed a positive association with hip circumference and low intake of this dietary pattern. Additionally, the presence of Bilophila spp. and Paraprevotella xylaniphila with high saturated fat and simple carbohydrate consumption showed a positive association with z-BMI, hip circumference, and waist circumference.
ARCHIVES OF MEDICAL RESEARCH
(2022)
Review
Immunology
Eleanor M. Townsend, Lucy Kelly, George Muscatt, Joshua D. Box, Nicole Hargraves, Daniel Lilley, Eleanor Jameson
Summary: The investigation of the human microbiome has revolutionized our understanding of the impact of microorganisms on human development and health. While most research has focused on bacteria and fungi, the exploration of gut viruses is still in its early stages. Bacteriophages, which influence bacterial populations in various ecosystems, remain relatively understudied in the context of the human gut microbiome.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Editorial Material
Gastroenterology & Hepatology
Emilie Viennois, Andrew T. Gewirtz, Benoit Chassaing
Article
Medicine, Research & Experimental
Christopher T. Fields, Benoit Chassaing, Geert J. de Vries
Summary: This article discusses the potential connection between gut microbiota and compulsive behavior, with a focus on the role of gut barrier dysfunction and type 2 inflammation. The study suggests that gut barrier dysfunction-associated type 2 inflammation may drive compulsive behavior through histamine regulation of dopamine neurotransmission. This highlights the possibility of targeting the gut in the treatment of compulsive behavior disorders.
MEDICAL HYPOTHESES
(2022)
Article
Sport Sciences
Marine Dupuit, Melanie Rance, Claire Morel, Patrice Bouillon, Audrey Boscaro, Vincent Martin, Emilie Vazeille, Nicolas Barnich, Benoit Chassaing, Nathalie Boisseau
Summary: High-intensity interval and resistance training can reduce abdominal/visceral fat in overweight or obese postmenopausal women and improve physical capacity. Training modifies the composition of intestinal microbiota, and the initial microbiota profile may affect the training response.
MEDICINE & SCIENCE IN SPORTS & EXERCISE
(2022)
Article
Microbiology
Robert H. Mills, Parambir S. Dulai, Yoshiki Vazquez-Baeza, Consuelo Sauceda, Noemie Daniel, Romana R. Gerner, Lakshmi E. Batachari, Mario Malfavon, Qiyun Zhu, Kelly Weldon, Greg Humphrey, Marvic Carrillo-Terrazas, Lindsay DeRight Goldasich, MacKenzie Bryant, Manuela Raffatellu, Robert A. Quinn, Andrew T. Gewirtz, Benoit Chassaing, Hiutung Chu, William J. Sandborn, Pieter C. Dorrestein, Rob Knight, David J. Gonzalez
Summary: Multi-omics analysis of faecal samples from patients with ulcerative colitis suggests a connection between Bacteroides vulgatus protease activity and the severity of disease symptoms. Understanding the disruption of host-microbiota interactions in UC is crucial for developing effective treatments. The study demonstrates that the overabundance of B. vulgatus proteases in a subset of UC patients contributes to disease activity. Targeting the protease activity could be a potential strategy for treating UC.
NATURE MICROBIOLOGY
(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
Stacey L. Heaver, Henry H. Le, Peijun Tang, Arnaud Basle, Claudia Mirretta Barone, Dai Long Vu, Jillian L. Waters, Jon Marles-Wright, Elizabeth L. Johnson, Dominic J. Campopiano, Ruth E. Ley
Summary: This study characterizes the pathways responsible for inositol lipid production in human gut Bacteroides and explores the importance of these lipids for capsule expression, antimicrobial peptide resistance, and colonization. The authors identify the biosynthetic pathway and enzymes involved in inositol lipid synthesis, and show that loss of inositol lipid production affects bacterial fitness and symbiosis in a mouse model. They also discover a previously undescribed pathway for bacterial PI-DAG synthesis. Overall, the findings suggest that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiotic relationships.
NATURE MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Taichi A. Suzuki, J. Liam Fitzstevens, Victor T. Schmidt, Hagay Enav, Kelsey E. Huus, Mirabeau Mbong Ngwese, Anne Griesshammer, Anne Pfleiderer, Bayode R. Adegbite, Jeannot F. Zinsou, Meral Esen, Thirumalaisamy P. Velavan, Ayola A. Adegnika, Le Huu Song, Timothy D. Spector, Amanda L. Muehlbauer, Nina Marchi, Hyena Kang, Lisa Maier, Ran Blekhman, Laure Segurel, GwangPyo Ko, Nicholas D. Youngblut, Peter Kremsner, Ruth E. Ley
Summary: The gut microbiomes of human populations worldwide have common core microbial species. However, within a species, certain strains show population specificity. This study suggests that humans and their gut microbes have experienced parallel evolutionary history, and specific microbial strains may play a crucial role in microbiome-mediated disease phenotypes.
Article
Gastroenterology & Hepatology
Noemie Daniel, Andrew T. Gewirtz, Benoit Chassaing
Summary: The study shows that the food additives carboxymethylcellulose (CMC) and polysorbate 80 (P80) can negatively impact intestinal microbiota, leading to chronic low-grade inflammation and metabolic dysregulations. However, daily administration of the probiotic Akkermansia muciniphila (A.muciniphila) can protect against the detrimental effects of these additives on both the microbiota and host. This study highlights the potential of using A.muciniphila as a probiotic to maintain intestinal and metabolic health.
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
Biochemical Research Methods
Albane Ruaud, Niklas Pfister, Ruth E. Ley, Nicholas D. Youngblut
Summary: Tree ensemble machine learning models are increasingly used in microbiome science due to their compatibility with the structure of sequence-based microbiome data. The endoR method simplifies and interprets these models, providing insights into the importance of features and their interactions. Through validations, endoR has shown comparable accuracy to other approaches and has been successfully applied to study the gut microbiome and identify associations between microbial taxa.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Clara Delaroque, Gary D. D. Wu, Charlene Compher, Josephine Ni, Lindsey Albenberg, Qing Liu, Yuan Tian, Andrew D. D. Patterson, James D. D. Lewis, Andrew T. T. Gewirtz, Benoit Chassaing
Summary: The study found that individual differences in diet and day-to-day variations in diet have a significant impact on the composition of the gut microbiota. Normalization of diet can reduce intra-individual variation and decrease the pro-inflammatory potential of the microbiota.
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
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.
Editorial Material
Gastroenterology & Hepatology
Jeremy Denizot, Benoit Chassaing
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Cell Biology
Noemie Daniel, Melanie Le Barz, Patricia L. Mitchell, Thibault V. Varin, Isabelle Bourdeau Julien, Dominique Farabos, Genevieve Pilon, Josee Gauthier, Carole Garofalo, Jing X. Kang, Jocelyn Trottier, Olivier Barbier, Denis Roy, Benoit Chassaing, Emile Levy, Frederic Raymond, Antonin Lamaziere, Nicolas Flamand, Cristoforo Silvestri, Christian Jobin, Vincenzo Di Marzo, Andre Marette
Summary: We compared endogenous omega-3 PUFA production to supplementation and found that endogenous production improved glucose intolerance and insulin resistance, while supplementation prevented hepatic steatosis but failed to improve insulin resistance.
