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
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
Gastroenterology & Hepatology
Shijia Hu, Eileen Png, Michelle Gowans, David E. H. Ong, Paola Florez de Sessions, Jie Song, Niranjan Nagarajan
Summary: This study characterized the gut and oral microbiome of Asian Crohn's disease (CD) patients using whole genome shotgun sequencing, revealing the enrichment of oral bacteria such as Streptococcus salivarius in the gut microbiome of CD patients. Additionally, distinct differences in gut microbial species abundance were observed between CD patients and healthy controls, with potential associations to disease activity. Ectopic gut colonization by oral bacteria was evidenced, especially during the active phase of CD, highlighting geographical/ethnic differences compared to subjects of European descent. Moreover, variations in microbial pathways provide potential targets for microbiome modification.
Article
Biology
Aniko Gal, Zoltan Grosz, Beata Borsos, Ildiko Szatmari, Agnes Sebok, Laszlo Javor, Veronika Harmath, Katalin Szakszon, Livia Dezsi, Eniko Balku, Zita Jobbagy, Agnes Herczegfalvi, Zsuzsanna Almassy, Levente Kerenyi, Maria Judit Molnar
Summary: Pompe disease is caused by a deficiency of lysosomal acid-alpha-glucosidase enzyme, leading to glycogen accumulation, resulting in late-onset and infantile-onset phenotypes. Enzymatic and genetic analysis of Hungarian patients revealed late-onset Pompe disease as more common, with the c.-32-13 T > G splice site alteration being the most prevalent pathogenic variant, affecting enzyme replacement therapy efficacy.
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)
Article
Transplantation
Noriaki Sato, Masanori Kakuta, Takanori Hasegawa, Rui Yamaguchi, Eiichiro Uchino, Koichi Murashita, Shigeyuki Nakaji, Seiya Imoto, Motoko Yanagita, Yasushi Okuno
Summary: By analyzing the differences in gut microbiome between diabetic and non-diabetic participants, the study found subtle changes in the gut microbiome of individuals with early CKD, with alterations related to short-chain fatty acid production already observable in early stages of CKD.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2021)
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)
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
Clinical Neurology
Joseph C. C. Boktor, Gil Sharon, Leo A. A. Verhagen Metman, Deborah A. A. Hall, Phillip A. A. Engen, Zoe Zreloff, Daniel J. J. Hakim, John W. W. Bostick, James Ousey, Danielle Lange, Gregory Humphrey, Gail Ackermann, Martha Carlin, Rob Knight, Ali Keshavarzian, Sarkis K. Mazmanian
Summary: This study analyzes the gut microbiome of patients with Parkinson's disease (PD) and controls, and finds significant alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products in PD patients. These changes may be related to disease progression.
MOVEMENT DISORDERS
(2023)
Article
Genetics & Heredity
Monica Y. Nino, Stijn L. M. in't Groen, Douglas O. S. de Faria, Marianne Hoogeveen-Westerveld, Hannerieke J. M. P. van den Hout, Ans T. van der Ploeg, Atze J. Bergsma, W. W. M. Pim Pijnappel
Summary: Patients with different common GAA genotypes exhibit a wide range of ages at symptom onset, indicating the presence of modifying factors that influence the disease progression. Additionally, certain genotypes were associated with earlier or later onset of symptoms, suggesting a complex interplay between genetic and environmental factors.
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
Immunology
Si Yu, Xiaomeng Ge, Hui Xu, Bei Tan, Bowen Tian, Yujie Shi, Yimin Dai, Yue Li, Songnian Hu, Jiaming Qian
Summary: This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. The results showed that IBD patients with CDI had decreased bacterial alpha diversity and significant differences in bacterial and fungal beta diversity compared to healthy individuals and IBD patients without CDI. Specific bacterial and fungal taxa were overrepresented in IBD patients with CDI. These findings provide insights into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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)