Review
Microbiology
Anissa M. Armet, Edward C. Deehan, Aidan F. O'Sullivan, Joao F. Mota, Catherine J. Field, Carla M. Prado, Alice J. Lucey, Jens Walter
Summary: Given the importance of the gut microbiota in the physiological effects of diet and chronic disease etiology, this review discusses contemporary nutritional recommendations from a microbiome science perspective. It also proposes integrating the microbiome into nutrition research to improve and innovate healthy eating.
CELL HOST & MICROBE
(2022)
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
Immunology
Joana Pereira-Dias, Chau Nguyen Ngoc Minh, Chau Tran Thi Hong, To Nguyen Thi Nguyen, Tuyen Ha Thanh, Caroline Zellmer, Hao Chung The, Lindsay Pike, Ellen E. Higginson, Stephen Baker
Summary: This study conducted shotgun metagenomic sequencing on fecal samples from healthy individuals in Vietnam and found a significant presence of antimicrobial resistance (AMR) genes in the gut microbiome, especially in young children. These genes could be transferred to pathogens, contributing to the generation of multidrug-resistant and extensively drug-resistant pathogens. Longitudinal cohort studies in urban and rural areas of developing countries are suggested to further understand the behavior of these AMR reservoirs.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Review
Endocrinology & Metabolism
Olivia D. Cooney, Prabhakar R. Nagareddy, Andrew J. Murphy, Man K. S. Lee
Summary: Probiotics have been highlighted for their role in modifying the gut microbiome, potentially reducing the severity of various chronic diseases and regulating bone mass. Targeting the gut microbiome may offer a potential alternative avenue for improving bone health, as gut-related diseases have been shown to impact bone health.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Microbiology
Evy Maas, John Penders, Koen Venema
Summary: Most studies on the human gut microbiota focus on bacteria, but recent research indicates that intestinal fungi are also important for maintaining health. This study analyzed the mycobiome of healthy individuals and its interaction with the bacterial component of the microbiome. The results showed a lower diversity of fungi compared to bacteria, with significant inter-individual variation. Positive correlations were observed between certain fungi and bacteria, including those associated with alleviating inflammatory bowel disease. Further research is needed to investigate the importance of these correlations and distinguish between gut colonizers and transient species.
Article
Multidisciplinary Sciences
Aaro Salosensaari, Ville Laitinen, Aki S. Havulinna, Guillaume Meric, Susan Cheng, Markus Perola, Liisa Valsta, Georg Alfthan, Michael Inouye, Jeramie D. Watrous, Tao Long, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Mohit Jain, Pekka Jousilahti, Veikko Salomaa, Rob Knight, Leo Lahti, Teemu Niiranen
Summary: The composition of gut microbiome is closely related to health and disease. Research has found that microbiome signatures related to the Enterobacteriaceae family are associated with cause-specific mortality risk in a well phenotyped Finish population over a 15-year follow-up.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Winston E. Anthony, Bin Wang, Kimberley Sukhum, Alaric W. D'Souza, Tiffany Hink, Candice Cass, Sondra Seiler, Kimberly A. Reske, Christopher Coon, Erik R. Dubberke, Carey-Ann D. Burnham, Gautam Dantas, Jennie H. Kwon
Summary: This study quantitatively analyzed the dynamics of the gut microbiota in healthy adult volunteers before, during, and 6 months after receiving antibiotic treatment. The results showed that antibiotics led to changes in species diversity, resistome, and metabolic output, and delayed the recovery of species richness. A subset of volunteers experienced a persistent reduction in microbiome diversity after antibiotics.
Article
Microbiology
Haitham Hajjo, Neerupma Bhardwaj, Tal Gefen, Naama Geva-Zatorsky
Summary: The COMBInatorial cliCK-chemistry (COMBICK) labeling method developed in this study allows for dynamic tracing of live, heterogeneous bacterial communities, including clinical isolates of the Enterobacteriaceae family. It has the potential to significantly advance mechanistic research in the microbiome field by enabling real-time studies of bacterial communities.
FRONTIERS IN MICROBIOLOGY
(2021)
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.
Article
Immunology
Andrea Rodenes-Gavidia, Araceli Lamelas, Sarah Bloor, Anthony Hobson, Sam Treadway, Jordan Haworth, Vineetha Vijayakumar, Malwina Naghibi, Richard Day, Empar Chenoll
Summary: This study investigated the effect of a 14-strain probiotic blend on the fecal microbiome of healthy adults. The results showed that while there were some compositional changes at the family and genus level, overall microbiome diversity did not change significantly.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Giulia Gibiino, Martina De Siena, Monica Sbrancia, Cecilia Binda, Vittorio Sambri, Antonio Gasbarrini, Carlo Fabbri
Summary: Diet plays a crucial role in influencing our intestinal microbiota and ecosystem balance, but a clearly defined dietary regime to ensure its health is still lacking. The Mediterranean diet may potentially have significant benefits for our health through direct interaction with our microbiota.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Tae Woong Whon, Hyun Sik Kim, Na-Ri Shin, Hojun Sung, Min-Soo Kim, Joon Yong Kim, Woorim Kang, Pil Soo Kim, Dong-Wook Hyun, Hoon Je Seong, Woo Jun Sul, Seong Woon Roh, Jin-Woo Bae
Summary: Neonatal calf diarrhea is a major cause of economic loss for cattle producers worldwide, with multifactorial etiology making disease control challenging. The study reveals microbial compositional and functional dysbiosis in the gut of diarrheic calves, potentially contributing to the onset of diarrhea. Additionally, it suggests that prolonged expansion of nontoxigenic Enterobacteriaceae in the gut may play a role in the development of calf diarrhea.
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)
Article
Microbiology
Ineta Kalnina, Dita Gudra, Ivars Silamikelis, Kristine Viksne, Ance Roga, Edmunds Skinderskis, Davids Fridmanis, Janis Klovins
Summary: This study investigates the relationship between the composition of the gut microbiome and variations in lipid profiles among healthy adults. The findings suggest that the gut microbiome plays a role in regulating host lipid metabolism, with different bacterial genera associated with different lipid patterns.
Article
Microbiology
Giovanni Vedel, Xavier Triado-Margarit, Olmo Linares, Jose Manuel Moreno-Rojas, Eva de la Pena, Ignacio Garcia-Bocanegra, Debora Jimenez-Martin, Juan Carranza, Emilio O. Casamayor
Summary: We surveyed the gut microbiota of wild boar populations using 16S rRNA gene analysis of fresh faeces, and found that diet, gender, and form status were major factors influencing the composition and diversity of the gut microbiota. The abundance of Enterobacteriaceae in the gut microbiota was associated with lower diversity, particularly in males. Additionally, we observed an inverse relationship between thoracic circumference and Enterobacteriaceae abundance in males. Continuous artificial feeding in hunting estates may negatively affect the gut microbiota and form status of wild boars.
MICROBIOLOGICAL RESEARCH
(2023)