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)
Review
Biology
Chenlin Hu, Piotr Rzymski
Summary: This article reviews the characteristics, phylogeny, distribution, and ecology of Melainabacteria and discusses their potential link to human health based on available human-microbiome studies.
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
Cell Biology
Sanzhima Garmaeva, Anastasia Gulyaeva, Trishla Sinha, Andrey N. Shkoporov, Adam G. Clooney, Stephen R. Stockdale, Johanne E. Spreckels, Thomas D. S. Sutton, Lorraine A. Draper, Bas E. Dutilh, Cisca Wijmenga, Alexander Kurilshikov, Jingyuan Fu, Colin Hill, Alexandra Zhernakova
Summary: The study found that there is a high diversity of gut virome composition in healthy adults, with individual viromes stable at the family level but varying significantly at the genera and species levels. Lower initial diversity of the human gut virome leads to a more pronounced effect of dietary intervention on its composition.
Article
Biochemistry & Molecular Biology
Shaqed Carasso, Bettina Fishman, Liel Stelmach Lask, Tamar Shochat, Naama Geva-Zatorsky, Eran Tauber
Summary: Each individual's chronotype, whether an early riser or a late sleeper, has a significant impact on the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. By analyzing the gut microbiome, distinct microbial signatures associated with different chronotypes were identified, suggesting the potential for developing dietary interventions to improve the health outcomes of late chronotypes.
Review
Microbiology
Ciara A. Tobin, Colin Hill, Andrey N. Shkoporov
Summary: The gut microbiome consists of a dense and metabolically active community of microorganisms and viruses in the lower gastrointestinal tract. Bacteria and their viruses are the most abundant members of the gut microbiome. Investigating their biology and interactions is crucial for understanding their roles in human health and disease. This review summarizes recent advances in understanding the taxonomic structure and ecological functions of the gut phageome, discussing the impact of age, diet, and geography on its composition. It also evaluates the potential link between changes in the gut phageome and diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, highlighting the need for standardization in research methods.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Review
Nutrition & Dietetics
Federica Bellerba, Valeria Muzio, Patrizia Gnagnarella, Federica Facciotti, Susanna Chiocca, Paolo Bossi, Diego Cortinovis, Ferdinando Chiaradonna, Davide Serrano, Sara Raimondi, Barbara Zerbato, Roberta Palorini, Stefania Canova, Aurora Gaeta, Sara Gandini
Summary: Recent evidence has shown that Vitamin D not only affects bones, but also plays a role in the immune system and is associated with the gut microbiota. Studies have found that VD supplementation significantly changes microbiome composition, particularly with the phyla Firmicutes, Actinobacteria, and Bacteroidetes.
Article
Gastroenterology & Hepatology
Muriel Derrien, Nadja Mikulic, Mary A. Uyoga, Empar Chenoll, Eric Climent, Adrian Howard-Varona, Suzane Nyilima, Nicole U. Stoffel, Simon Karanja, Robert Kottler, Bernd Stahl, Michael B. Zimmermann, Raphaelle Bourdet-Sicard
Summary: The gut microbiome of 6- to 11-month-old Kenyan infants is characterized by a high prevalence of Bifidobacterium longum, particularly the subspecies B. infantis. The composition and functional features of the gut microbiome are associated with the prevalence of specific human milk oligosaccharide groups.
Article
Immunology
Shih-Chen Fu, Chung-Han Lee, Yi-Chen Hsieh, Pei-Hua Wu, Sheng-Hsuan Lin, Hsiuying Wang
Summary: This study suggests that discomfort induced by entacapone may be related to shifts in microbial composition, leading to gastrointestinal problems and other side effects. Manipulation of gut microbiota could potentially reduce these unpleasant effects in the long term.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Nutrition & Dietetics
Hala Elzayat, Ghaidaa Mesto, Farah Al-Marzooq
Summary: Inflammatory bowel disease (IBD) is a complex disorder characterized by chronic inflammation of the gastrointestinal tract (GIT). Recent research has shown the significant role of the oral and gut microbiome in the development and progression of IBD and their impact on overall gut health. The interconnected oral and gut microbiome, as complex microbial communities, are implicated in IBD pathogenesis, and understanding their relationship can provide insights into disease management and prevention strategies.
Article
Biochemical Research Methods
Fenglong Yang, Quan Zou, Bo Gao
Summary: This study highlights the compositional nature of microbiome data and introduces the distal discriminative balance analysis method for building balance-based models for human gut microbiome-related diseases. The concept of balance-disease associations is emphasized, leading to the development of the Human Gut Balance-Disease Association Database (GBDAD). The inference of balance-based species-disease associations can accelerate the generation of new microbe-disease association hypotheses in gastrointestinal microecology research and clinical trials.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Rafael R. C. Cuadrat, Tobias Goris, Anna Birukov, Fabian Eichelmann, Bruno G. N. Andrade, Corinna Bang, Andre Franke, Clemens Wittenbecher, Matthias B. B. Schulze
Summary: This study found a correlation between gut microbiota and vascular stiffness, suggesting a potential role of individual components of the gut microbiota in the development of vascular stiffness.
SCIENTIFIC REPORTS
(2023)
Article
Allergy
Kathleen Lee-Sarwar, Sandra Dedrick, Babak Momeni, Rachel S. Kelly, Robert S. Zeiger, George T. O'Connor, Megan T. Sandel, Leonard B. Bacharier, Avraham Beigelman, Nancy Laranjo, Diane R. Gold, Jessica Lasky-Su, Augusto A. Litonjua, Yang-Yu Liu, Scott T. Weiss
Summary: This study analyzed the relationship between gut microbiome and metabolome and wheeze frequency in children with asthma. The results showed that specific microbial taxa and metabolites were associated with high wheeze proportion in children. This finding suggests the impact of the gut microbiome on asthma morbidity in children.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Microbiology
Patricia G. Wolf, Elise S. Cowley, Adam Breister, Sarah Matatov, Luke Lucio, Paige Polak, Jason M. Ridlon, H. Rex Gaskins, Karthik Anantharaman
Summary: This study reveals that microbial sulfur metabolism in the human gut is more diverse and prevalent than previously known, and is statistically associated with colorectal cancer. The study also identifies new microbial genera associated with reductive taurine metabolism. Furthermore, the findings highlight the importance of organic sulfur substrates as a major source of H2S in the human gut.
Article
Gastroenterology & Hepatology
Brandilyn A. Peters, Qibin Qi, Mykhaylo Usyk, Martha L. Daviglus, Jianwen Cai, Nora Franceschini, James P. Lash, Marc D. Gellman, Bing Yu, Eric Boerwinkle, Rob Knight, Robert D. Burk, Robert C. Kaplan
Summary: This study found that there is an association between kidney function and the gut microbiome. The relationship between kidney damage and the gut microbiome depends on whether the individual has diabetes. The metabolites produced by the gut microbiome may contribute to the progression of chronic kidney disease.
