Review
Biochemistry & Molecular Biology
Andrea Piccioni, Federico Rosa, Federica Manca, Giulia Pignataro, Christian Zanza, Gabriele Savioli, Marcello Covino, Veronica Ojetti, Antonio Gasbarrini, Francesco Franceschi, Marcello Candelli
Summary: The composition of the human microbiome plays a crucial role in health, and alterations in the microbiota can lead to Clostridium difficile infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Nutrition & Dietetics
Lynnette Ferguson, Matthew Barnett
Summary: Nutrigenomics New Zealand (NuNZ) was a collaborative research programme established by three organizations with the aim of studying the application of nutrigenomics in New Zealand and exploring its potential benefits in the plant food and agricultural sectors. The programme divided nutrigenomics into personalized nutrition and nutrigenomics, utilizing various science laboratories for comprehensive analysis to understand the impact of food products and diets on health.
Review
Immunology
Denis A. Mogilenko, Alexey Sergushichev, Maxim N. Artyomov
Summary: Immunometabolism has become a new interdisciplinary field of research in recent years, providing important insights into the regulation of immune responses. Traditional approaches and new technologies, such as spatially resolved metabolic imaging and computational algorithms, have helped us understand the complexity of immunometabolic regulation. This review discusses recent studies and technological developments that aim to capture the interplay between immune responses and metabolism.
ANNUAL REVIEW OF IMMUNOLOGY
(2023)
Review
Plant Sciences
Muhammad-Redha Abdullah-Zawawi, Nisha Govender, Sarahani Harun, Nor Azlan Nor Muhammad, Zamri Zainal, Zeti-Azura Mohamed-Hussein
Summary: Omics technologies are used to understand the complexity of plant systems and components. Integration of multi-omics datasets allows for comprehensive understanding of organism life processes. Open-source datasets and computational tools aid in silico functional prediction of unknown genes, proteins, and metabolites. The systems biology approach involves data collection, modeling, experimentation, and hypothesis generation for validation. Informatics technologies enhance gene function prediction at a minimal cost and effort. This article provides a comprehensive view and resources for gene function prediction in plants.
Article
Gastroenterology & Hepatology
Hongliang Tian, Jiaqu Cui, Chen Ye, Jiangman Zhao, Bo Yang, Yue Xu, Shushen Ji, Le Wang, Xiaoqiong Lv, Chunlian Ma, Shailan Zhou, Ning Li, Xinjun Wang, Huanlong Qin, Qiyi Chen
Summary: Approximately 10% of CDI patients exhibit resistance to FMT and the mechanisms behind this are still unknown. This study focused on investigating the microbiome profile in FMT-refractory patients with rCDI. Through rigorous screening and analysis, the study found that non-remission patients had significantly reduced α-diversity indexes and depleted abundance of key butyrate-producing Firmicutes bacteria. On the other hand, patients with a favorable FMT response had a higher abundance of Veillonella prior to treatment.
Article
Pediatrics
Ryan M. Hanson, Amy J. Wagner
Summary: Severe, complicated Clostridium difficile colitis is rare in pediatric patients and little is known about its medical and surgical management in this population. A case report of a 15-year-old female patient with severe, complicated C difficile colitis successfully treated with diverting loop ileostomy and colonic lavage is presented. This approach, instead of subtotal colectomy and end ileostomy, should be considered as an alternative for pediatric patients with severe, complicated C difficile colitis.
Review
Immunology
Daniel O'Connor
Summary: Vaccines have had a significant impact on child health, but the immunological processes involved are not fully understood. Recent technological advances offer the opportunity to reveal the immunology underlying vaccine response, potentially revolutionizing vaccine development and testing.
EXPERT REVIEW OF VACCINES
(2022)
Article
Cardiac & Cardiovascular Systems
Andrew A. Gibb, Emma K. Murray, Deborah M. Eaton, Anh T. Huynh, Dhanendra Tomar, Joanne F. Garbincius, Devin W. Kolmetzky, Remus M. Berretta, Markus Wallner, Steven R. Houser, John W. Elrod
Summary: The authors used systems biology to study metabolic and transcriptional changes in a large animal model of HFpEF, finding alterations in oxidative metabolism and mitochondrial dysfunction. These findings provide insights into the cellular biology underlying the progression of HFpEF.
JACC-BASIC TO TRANSLATIONAL SCIENCE
(2021)
Review
Medicine, General & Internal
Ibrahim A. Al-Zahrani
Summary: Clostridioides difficile (C. difficile) infection is a global threat to many healthcare settings. Excessive use of antimicrobials, lack of optimal antibiotic policies, and suboptimal infection control practices have fueled the development of this health issue. Prudent use of antimicrobials and simple infection control measures can significantly reduce infection rates.
SAUDI MEDICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Nguyen Thi Hai Yen, Jung-Hwa Oh, Nguyen Thi Van Anh, Quoc-Viet Le, Se-Myo Park, Young Jin Park, Yong-Soon Cho, Kyoung-Sik Moon, Huy Truong Nguyen, Jae-Gook Shin, Nguyen Phuoc Long, Dong Hyun
Summary: This study conducted multi-specimen molecular characterization in rats treated with different doses of indomethacin to investigate its toxicity mechanism. The results showed that a dose of 10 mg/kg of indomethacin caused significant metabolic changes and kidney injury. Analysis revealed an oxidant-antioxidant imbalance and dysfunction of mitochondria, which resulted in the dysregulation of metabolites and genes related to the kidney, as well as the suppression of amino acid and fatty acid metabolism. These findings provide insights into the mechanism of indomethacin toxicity and suggest potential targets for reducing its toxicity.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Surgery
Austin M. Eckhoff, Ashton A. Connor, Julie K. M. Thacker, Dan G. Blazer, Harvey G. Moore, Randall P. Scheri, Sandhya A. Lagoo-Deenadayalan, David H. Harpole, Keri A. Seymour, J. Todd Purves, Kadiyala V. Ravindra, Kevin W. Southerland, Daniel J. Rocke, Jennifer B. Gilner, Daniel C. Parker, James R. Bain, Michael J. Muehlbauer, Olga R. Ilkayeva, David L. Corcoran, Jennifer L. Modliszewski, Nicolas Devos, Matthew W. Foster, M. Arthur Moseley, Holly K. Dressman, Cliburn Chan, Janet L. Huebner, Scott Chasse, Linda Stempora, Mary E. Aschenbrenner, Mary-Beth Joshi, Beth Hollister, Ricardo Henao, Richard T. Barfield, Mark A. Ellison, Sean Bailey, Stephen Woody, Erich S. Huang, Allan Kirk, E. Shelley Hwang
Summary: The project aims to design a prospective biospecimen repository that integrates clinical data and multi-omics assays to study controlled injury and healing mechanisms. Methods involve collecting samples from patients undergoing 14 surgeries and utilizing genomic, transcriptomic, proteomic, and metabolomic assays to describe their responses to injury.
Article
Microbiology
Jennifer J. Dawkins, Jessica R. Allegretti, Travis E. Gibson, Emma McClure, Mary Delaney, Lynn Bry, Georg K. Gerber
Summary: This study conducted a longitudinal analysis of the gut microbiome and metabolome changes in patients with primary Clostridioides difficile infection (CDI). The results showed that metabolomic data can accurately predict the recurrence of CDI, providing important insights for the development of diagnostic tests and treatments.
Article
Microbiology
Rachita K. Kumar, Nitin Kumar Singh, Sanjaay Balakrishnan, Ceth W. Parker, Karthik Raman, Kasthuri Venkateswaran
Summary: This study predicts possible metabolic interactions in the ISS microbiome using a computational approach and sheds further light on its organization. The results show beneficial interactions between Klebsiella pneumoniae and Pantoea genus, and parasitic and amensalistic interactions between Klebsiella pneumoniae and Aspergillus and Penicillium species. Klebsiella pneumoniae has positive effects on the survival of other microorganisms, but may also have negative interactions with potential pathogens.
Review
Biochemistry & Molecular Biology
Stuart L. Rulten, Richard P. Grose, Susanne A. Gatz, J. Louise Jones, Angus J. M. Cameron
Summary: Our understanding of cancer has advanced rapidly, recognizing the variation between patients and leading to precision medicines that promise maximum efficacy, safety, and reduced costs. However, many patients still lack access to these personalized treatments, highlighting the need for new disease characteristics, accurate diagnosis, better clinical trials, and global accessibility to targeted therapies. This review discusses current technological trends and multidisciplinary efforts to ensure wider implementation of precision oncology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ecology
Stefanie Widder, Jiangchao Zhao, Lisa A. Carmody, Qingyang Zhang, Linda M. Kalikin, Patrick D. Schloss, John J. LiPuma
Summary: In this study, bacterial communities in the airways of cystic fibrosis patients were analyzed, leading to the identification of different pulmotypes which show temporal sequence patterns and significant correlations with patient clinical status. By constructing pulmotype-specific metabolic activity profiles, it was found that microbial communities within pulmotypes drive distinct community functions.
Article
Microbiology
Courtney R. Armour, Begum D. Topcuoglu, Andrea Garretto, Patrick D. Schloss
Summary: Colorectal cancer, a common and deadly disease in the United States, can be effectively prevented with early detection and treatment. The gut microbiome has shown promise as a noninvasive method for detecting colorectal cancer. In this study, researchers investigated the optimal taxonomic resolution for microbiome-based classification of colorectal cancer and found that mid-range resolution (family, genus, and OTU) provides the best prediction performance.
Article
Microbiology
Kelly L. Sovacool, Sarah L. Westcott, M. Brodie Mumphrey, Gabrielle A. Dotson, Patrick D. Schloss
Summary: Advancements in DNA sequencing technology have allowed researchers to generate millions of sequence reads from microorganisms. Efficient software tools are needed to assign microbial sequences into taxonomic groups. Existing methods either produce inconsistent results or have reduced quality. To address this, we developed OptiFit, a new algorithm that allows for consistent and high-quality assignments, making it easier to compare different studies or add new data to existing studies.
Article
Oncology
Rosa Klotz, Magdalena Holze, Colette Doerr-Harim, Erich Grohmann, Barbara Nied, Burkhard Lebert, Susanne Weg-Remers, Claudia Lutz, Karin Meissler, Patrick Schloss, Charlotte Ullrich, Susanne Frankenhauser, Heidi Lutter, Diedrich Buehler, Azaz Ahmed, Toto Gronlund, Andre L. Mihaljevic
Summary: This study aimed to identify and prioritize unresolved research questions related to colorectal cancer through collaboration with relevant stakeholders. Through nationwide surveys and a consensus workshop, the top 10 research topics were determined to provide researchers and funding bodies with directions for patient-relevant research projects.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Microbiology
Madeline R. Barron, Kelly L. Sovacool, Lisa Abernathy-Close, Kimberly C. Vendrov, Alexandra K. Standke, Ingrid L. Bergin, Patrick D. Schloss, Vincent B. Young
Summary: Patients with inflammatory bowel disease (IBD) have an increased risk of developing C. difficile infection (CDI), even in the absence of antibiotic treatment. The mechanisms regulating C. difficile colonization in IBD patients remain unclear. In this study, a mouse model was used to demonstrate that intestinal inflammation alters microbiota composition, leading to susceptibility to C. difficile colonization. Treating inflammation with an anti-p40 monoclonal antibody restores colonization resistance. Microbiota transfer experiments confirm that the microbiota shaped in the setting of IBD is the primary driver of susceptibility to C. difficile colonization.
Article
Microbiology
Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss
Summary: Clostridioides difficile colonization can lead to a range of infection severities, from mild diarrhea to life-threatening conditions. While factors such as patient age, blood cell count, and C. difficile characteristics have been associated with disease severity, the role of specific gut bacteria in influencing severity is unclear. This study demonstrates that different gut bacterial communities can contribute to variations in Clostridioides difficile infection outcomes. Certain bacterial groups were associated with more severe outcomes, while others were associated with milder outcomes. Incorporating gut bacterial community data into severity models may aid in identifying at-risk patients and improving interventions.
Article
Microbiology
Nicholas A. Lesniak, Sarah Tomkovich, Andrew Henry, Ana Taylor, Joanna Colovas, Lucas Bishop, Kathryn McBride, Patrick D. Schloss
Summary: Antibiotic use is a major risk factor for Clostridioides difficile infection (CDI). Fecal microbiota transplant can restore gut bacterial community and eliminate the infection. This study explored the potential of using fecal community transplant to prevent CDI and found that it can prevent or clear C. difficile.
Article
Public, Environmental & Occupational Health
Meghana Kamineni, Erkin Otles Meng, Jeeheh Oh, Krishna Rao, Vincent B. Young, Benjamin Y. Li, Lauren R. West, David C. Hooper, Erica S. Shenoy, John G. Guttag, Jenna Wiens, Maggie Makar
Summary: This article presents the prospective and retrospective evaluations of two CDI infection risk prediction models and discusses their robustness to data-set shifts.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Microbiology
Patrick D. Schloss
Summary: The Riffomonas YouTube channel is dedicated to teaching scientists and others how to conduct reproducible research using modern data science tools, bridging the gap between those familiar with laboratory research and the methods of data analysis.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Behavioral Sciences
Anne C. Sabol, William L. Close, Lauren Petrullo, Connor T. Lambert, Brian Keane, Nancy G. Solomon, Patrick D. Schloss, Ben Dantzer
Summary: The sociality of prairie voles does not affect the diversity of their oral microbiome, which contrasts with studies predominantly conducted on primates and gut microbiome. This highlights the importance of investigating other microbiome regions and relationships in different species.
Article
Oncology
S. B. Rifkin, M. A. Sze, K. Tuck, E. Koeppe, E. M. Stoffel, P. D. Schloss
Summary: This study investigated the association between microbiome and CRC risk in Lynch syndrome (LS). The results showed significant differences in microbiome composition between LS and non-LS, with specific taxa differences observed in LS-CRC patients. However, larger prospective studies are needed to determine if microbiome composition contributes to CRN development in LS patients.
JOURNAL OF GASTROINTESTINAL CANCER
(2023)
Editorial Material
Microbiology
Patrick D. Schloss, Christina A. Cuomo
MICROBIOLOGY SPECTRUM
(2023)
Article
Gastroenterology & Hepatology
Patricia P. Bloom, Krishna Rao, Christine Bassis, Borko Nojkov, Vincent B. Young, Anna S. F. Lok
Summary: Patients with cirrhosis have higher duodenal epithelial permeability and lower mucosal bacteria alpha diversity compared to controls, while no such differences are seen in the ileum or colon. Specific bacteria are associated with epithelial permeability and future hepatic decompensation.
HEPATOLOGY COMMUNICATIONS
(2023)
Article
Microbiology
Patrick D. Schloss
Summary: Published in 2014, the study by McMurdie and Holmes examines how to control for the unavoidable uneven sequencing depths in 16S rRNA gene sequencing. Their findings have significantly impacted the methods used by microbiome researchers. However, there are several issues with the design and analysis of their simulations that compromise their results. When reproducing and expanding upon their analysis, it becomes clear that rarefaction is actually the most robust approach for controlling uneven sequencing effort across samples.