Article
Microbiology
Fabrice Jean-Pierre, Arsh Vyas, Thomas H. Hampton, Michael A. Henson, George A. O'Toole
Summary: Culture-independent studies have shown that chronic lung infections in persons with cystic fibrosis involve diverse microbial communities. Interactions among these communities influence clinical outcomes, and a single community cannot fully explain the diversity of outcomes. Combining computational and experimental approaches can help enhance our understanding of microbial community function and lead to the identification of new therapeutics for polymicrobial infections.
Article
Immunology
Zaina Inam, Erin Felton, Aszia Burrell, Hollis Chaney, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Edith T. Zemanick, Keith A. Crandall, Andrea Hahn
Summary: In CF patients, despite an increase in recurrent exacerbations and antibiotic treatments, PEx events did not lead to changes in microbial diversity but were associated with changes in lung function. Specifically, over time, microbial diversity increased in the lung microbiome, while bacterial richness remained stable.
OPEN FORUM INFECTIOUS DISEASES
(2022)
Review
Biology
Filippo Scialo, Felice Amato, Gustavo Cernera, Monica Gelzo, Federica Zarrilli, Marika Comegna, Lucio Pastore, Andrea Bianco, Giuseppe Castaldo
Summary: The defective mucociliary clearance in CF patients due to CFTR malfunctioning predisposes them to colonization by pathogens, leading to recurrent inflammation and rapid deterioration of lung function, impacting the lung microbiome composition. Understanding of microbial interactions in the lung and how they change during disease progression is still in its early stages, but manipulating the lung microbiome could offer promising prospects for improving therapies for CF patients.
Review
Infectious Diseases
Evanthia P. Perikleous, Despoina Gkentzi, Aris Bertzouanis, Emmanouil Paraskakis, Aleksandar Sovtic, Sotirios Fouzas
Summary: Patients with cystic fibrosis (CF) are frequently exposed to antibiotics, which can contribute to the development of antimicrobial resistance (AMR) and make treatment challenging. Conventional susceptibility-testing techniques may not accurately assess AMR in the lungs, and the dosing of antibiotics is complicated by factors such as biofilm formation and lung penetration. Novel diagnostic tools and effective treatment strategies are urgently needed to address the growing problem of AMR in CF.
Article
Immunology
Conan Y. Zhao, Yiqi Hao, Yifei Wang, John J. Varga, Arlene A. Stecenko, Joanna B. Goldberg, Sam P. Brown
Summary: The study found that models trained on whole-microbiome quantitation outperformed models trained only on pathogen quantitation in lung infections in people with cystic fibrosis. The most accurate models retained key pathogens and nonpathogen taxa as important predictors of lung health.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Respiratory System
Wen-Wen Wang, Bei Mao, Yang Liu, Shu-Yi Gu, Hai-Wen Lu, Jiu-Wu Bai, Shuo Liang, Jia-Wei Yang, Jian-Xiong Li, Xiao Su, Hai-Yang Hu, Chen Wang, Jin-Fu Xu
Summary: This study utilized a multi-omics approach to identify differences in gut microbiota and metabolic profiles between bronchiectasis patients and healthy volunteers. It revealed the potential of gut microbiota as biomarkers for bronchiectasis.
RESPIRATORY RESEARCH
(2022)
Article
Health Care Sciences & Services
Xiubin Liang, Mohamad Bouhamdan, Xia Hou, Kezhong Zhang, Jun Song, Ke Hao, Jian-Ping Jin, Zhongyang Zhang, Jie Xu
Summary: The study identified a new CF animal model that exhibits intestinal dysbiosis phenotype, which may facilitate research and development of novel treatments for CF-associated gastrointestinal diseases. The fecal microbiomes of CF rabbits showed lower richness and diversity compared to wild-type rabbits, indicating significant taxonomic and functional dysbiosis.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Environmental Sciences
Siew Shing Wei, Choo Mei Yen, Ian P. G. Marshall, Hazrulrizawati Abd Hamid, Shamrulazhar Shamzir Kamal, Dennis Sandris Nielsen, Hajar Fauzan Ahmad
Summary: Antibiotic contamination in the marine environment poses a emerging threat to marine ecosystems. This study compared the gut and coelomic microbiota of Stichopus ocellatus with sediments from two coastal districts of Pahang, potentially serving as biomarkers for sediment pollution monitoring. The bacterial communities in the gut and sediment samples differed significantly both within and between the samples. Vibrio genera dominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera dominated in Pekan samples. Vibrio parahaemolyticus in sediment and gut samples exhibited resistance genes against tetracycline and beta-lactam antibiotics.
MARINE POLLUTION BULLETIN
(2022)
Article
Microbiology
Nicole Acosta, Christina S. Thornton, Michael G. Surette, Ranjani Somayaji, Laura Rossi, Harvey R. Rabin, Michael D. Parkins
Summary: The study found that azithromycin treatment did not lead to significant changes in the CF microbiome structure. However, the baseline community structure was found to be associated with the subsequent response to azithromycin in CF adults.
Article
Microbiology
Jacob Vieira, Sirus Jesudasen, Lindsay Bringhurst, Hui-Yu Sui, Lauren McIver, Katrine Whiteson, Kurt Hanselmann, George A. O'Toole, Christopher J. Richards, Leonard Sicilian, Isabel Neuringer, Peggy S. Lai
Summary: This study found that increased oxygen in persons with cystic fibrosis led to reduced total numbers and diversity of microbes, while common CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus were relatively spared. Supplemental oxygen use may promote the growth of lung pathogens and should be further studied in the clinical setting.
Article
Gastroenterology & Hepatology
Isabelle McKay, Josie van Dorst, Tamarah Katz, Michael Doumit, Bernadette Prentice, Louisa Owens, Yvonne Belessis, Sandra Chuang, Adam Jaffe, Torsten Thomas, Michael Coffey, Chee Y. Ooi
Summary: This study conducted a comprehensive analysis of diet and microbiota in children with CF, finding significant changes in intestinal inflammation and respiratory and gastrointestinal microbiota compared to children without CF. It also identified correlations between gastrointestinal and respiratory microbiota, lung function, CF pulmonary exacerbations, and anthropometrics, supporting the concept of an altered gut-lung axis in children with CF. Additionally, significant differences in dietary quality were found, with CF children consuming higher proportions of fats and lower proportions of carbohydrates, wholegrains, fiber, insoluble fiber, starch, and resistant starch.
Article
Infectious Diseases
Arianna Pani, Valeria Lucini, Silvana Dugnani, Alice Schianchi, Francesco Scaglione
Summary: This study evaluates the effect of antibiotics used for aerosol therapy in CF on the production of LOX in P. aeruginosa, and finds that levofloxacin and amikacin have inhibitory activity on LOX secretion.
Review
Gastroenterology & Hepatology
Brent Gilbert, Gerard Kaiko, Stephen Smith, Peter Wark
Summary: Cystic fibrosis (CF) is a hereditary, life-limiting, multi-system condition that results in chronic respiratory infections, pancreatic insufficiency and intestinal inflammation. Evidence indicates that CF patients develop colorectal cancer (CRC) earlier and more often than the general population. Intestinal dysbiosis resulting from genetics and CF treatment is a contributing factor.
COLORECTAL DISEASE
(2023)
Article
Immunology
Jonathan D. Cogen, Anna Faino, Frankline Onchiri, Lucas R. Hoffman, Matthew P. Kronman, David P. Nichols, Margaret Rosenfeld, Ronald L. Gibson
Summary: A retrospective cohort study found that there were no significant differences in respiratory and clinical outcomes between young patients with cystic fibrosis treated with one versus two intravenous antipseudomonal antibiotics for pulmonary exacerbations.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Microbiology
Claudie Lamoureux, Charles-Antoine Guilloux, Elise Courteboeuf, Stephanie Gouriou, Clemence Beauruelle, Genevieve Hery-Arnaud
Summary: Resistance to certain antibiotics was observed in a significant percentage of isolates from the predominant anaerobic species in the respiratory microbiota of patients with cystic fibrosis, potentially exacerbated by long-term antibiotic therapy. A positive correlation was found between resistance to clindamycin and chronic azithromycin administration. Further characterization of the anaerobic resistome at the species level is needed to prevent the emergence of resistance within lung microbiota.
Article
Biology
J. Liu, Xinlian Zhang, T. Chen, T. Wu, T. Lin, L. Jiang, S. Lang, L. Liu, L. Natarajan, J. X. Tu, T. Kosciolek, J. Morton, T. T. Nguyen, B. Schnabl, R. Knight, C. Feng, Y. Zhong, X. M. Tu
Summary: This paper proposes a new approach to model beta-diversity using functional response models, addressing limitations of current methods for beta-diversity and providing a premise for future extension to longitudinal and other clustered data. The approach is illustrated with both real and simulated data.
Article
Obstetrics & Gynecology
Carrie E. Jung, Mehrbod Estaki, Jessica Chopyk, Bryn C. Taylor, Antonio Gonzalez, Daniel McDonald, Jenny Shin, Kimberly Ferrante, Erika Wasenda, Quinn Lippmann, Rob Knight, David Pride, Emily S. Lukacz
Summary: In postmenopausal women with recurrent urinary tract infections, the urogenital microbiome showed an increase in Lactobacillus after 6 months of vaginal estrogen treatment. Specifically, the relative increase in L. crispatus may be associated with treatment success.
FEMALE PELVIC MEDICINE AND RECONSTRUCTIVE SURGERY
(2022)
Article
Gastroenterology & Hepatology
Qibin Qi, Jun Li, Bing Yu, Jee-Young Moon, Jin C. Chai, Jordi Merino, Je Hu, Miguel Ruiz-Canela, Casey Rebholz, Zheng Wang, Mykhaylo Usyk, Guo-Chong Chen, Bianca C. Porneala, Wenshuang Wang, Ngoc Quynh Nguyen, Elena Feofanova, Megan L. Grove, Thomas J. Wang, Robert E. Gerszten, Josee Dupuis, Jordi Salas-Salvado, Wei Bao, David L. Perkins, Mariha L. Daviglus, Bharat Thyagarijan, Jianwen Cai, Tao Wang, JoAnn E. Manson, Miguel A. Martinez-Gonzalez, Elizabeth Selvin, Kathryn M. Rexrode, Clary B. Clish, Frank B. Hu, James B. Meigs, Rob Knight, Robert D. Burk, Eric Boerwinkle, Robert C. Kaplan
Summary: The study found positive associations between tryptophan and its metabolites with the risk of type 2 diabetes, while indolepropionate was inversely associated with the risk. Additionally, host genetic variants, dietary factors, gut bacteria, and their interplay related to these type 2 diabetes-related metabolites were identified.
Article
Clinical Neurology
Ronald J. Ellis, Robert K. Heaton, Sara Gianella, Gibraan Rahman, Rob Knight
Summary: The analysis of gut microbial diversity and dysbiosis in PWH and PWoH revealed that more severe DNP was associated with lower alpha diversity in PWH. Specific changes in microbial taxa ratios were also observed in PWH with DNP. These findings suggest that gut dysbiosis may contribute to prevalent DNP in PWH.
Article
Cell Biology
Yang Liu, Guillaume Meric, Aki S. Havulinna, Shu Mei Teo, Fredrik Aberg, Matti Ruuskanen, Jon Sanders, Qiyun Zhu, Anupriya Tripathi, Karin Verspoor, Susan Cheng, Mohit Jain, Pekka Jousilahti, Yoshiki Vazquez-Baeza, Rohit Loomba, Leo Lahti, Teemu Niiranen, Veikko Salomaa, Rob Knight, Michael Inouye
Summary: In this study, the predictive capacity of gut microbial predictors alone and in combination with conventional risk factors for liver disease was assessed using machine learning. The results showed that gut microbiota had comparable predictive capacity to conventional factors, and the performance was significantly improved when microbiome was combined with conventional risk factors using machine learning.
Meeting Abstract
Biochemistry & Molecular Biology
Nathan Greenberg, Marissa L. Burnsed-Torres, Antonio Gonzalez, Abigail G. Casso, Kara L. Lubieniecki, Brian P. Ziemba, Matthew J. Rossman, Emily C. Adam, Michel Chonchol
Article
Nutrition & Dietetics
Julia Beauchamp-Walters, Gajender Aleti, Lourdes Herrera, Justine Debelius, Natalie Lima, Pritha Dalal, Suzi Hong, Rob Knight, Kyung E. Rhee
Summary: This study aimed to examine the relationship between diet and the gut microbiome in children with medical complexity (CMC) who receive enteral tube feedings, and to determine the impact of different formulas on the CMC microbiome. The results showed that CMC receiving exclusive enteral nutrition had decreased alpha diversity and differences in beta diversity compared with healthy controls, highlighting the importance of diet over medications.
JOURNAL OF PARENTERAL AND ENTERAL NUTRITION
(2023)
Editorial Material
Biochemical Research Methods
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri Porozov, Tetyana Vasylyeva, Joel O. Wertheim, Braden T. Tierney, Charles Y. Chiu, Ren Sun, Aiping Wu, Malak S. Abedalthagafi, Victoria M. Pak, Shivashankar H. Nagaraj, Adam L. Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E. Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C. Wu, Alex Zelikovsky, Rob Knight, Keith A. Crandall, Serghei Mangul
Summary: During the COVID-19 pandemic, genomics and bioinformatics have become crucial tools in public health. They have been used to acquire genomic data that support global health responses, aid in the development of testing methods, and enable the timely tracking of novel SARS-CoV-2 variants. However, the rapid generation and analysis of genomic data present unique technical, scientific, and organizational challenges.
Article
Microbiology
Cameron Martino, Daniel McDonald, Kalen Cantrell, Amanda Hazel Dilmore, Yoshiki Vazquez-Baeza, Liat Shenhav, Justin P. Shaffer, Gibraan Rahman, George Armstrong, Celeste Allaband, Se Jin Song, Rob Knight
Summary: Microbiome data analysis is challenging due to the specific characteristics of sparsity and compositionality. Incorporating phylogenetic information into robust principal-component analysis and compositional tensor factorization methods significantly improves the discriminatory power of clustering and the classification accuracy. This strategy demonstrates improvements in effect size and clustering accuracy for both simulated and real microbiome data.
Article
Microbiology
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vazquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Meric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight
Summary: The operational genomic unit (OGU) method directly exploits sequence alignment hits to individual reference genomes for assessing microbial community diversity and relevance to environmental factors, offering maximal resolution of community composition and supporting phylogenetic methods. The method outperforms taxonomic unit-based analyses in informing biologically relevant insights, as demonstrated in real-world case studies.
Article
Oncology
Zeni Wu, Doratha A. Byrd, Yunhu Wan, Daniel Ansong, Joe-Nat Clegg-Lamptey, Beatrice Wiafe-Addai, Lawrence Edusei, Ernest Adjei, Nicholas Titiloye, Florence Dedey, Francis Aitpillah, Joseph Oppong, Verna Vanderpuye, Ernest Osei-Bonsu, Casey L. Dagnall, Kristine Jones, Amy Hutchinson, Belynda D. Hicks, Thomas U. Ahearn, Jianxin Shi, Rob Knight, Richard Biritwum, Joel Yarney, Seth Wiafe, Baffour Awuah, Kofi Nyarko, Jonine D. Figueroa, Rashmi Sinha, Montserrat Garcia-Closas, Louise A. Brinton, Emily Vogtmann
Summary: The oral microbiome is associated with breast cancer and nonmalignant breast disease, and its diversity is negatively correlated with the risk of these conditions. There is a strong correlation between the oral and fecal microbiome in breast cancer cases, but not in controls.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Biotechnology & Applied Microbiology
Julia M. Gauglitz, Kiana A. West, Wout Bittremieux, Candace L. Williams, Kelly C. Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M. Aceves, Elizabeth Brown, Nicole C. Sikora, Alan K. Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J. Meehan, Kathleen Dorrestein, Justin P. Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J. Johnson, Katharina Spengler, Pedro Belda-Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O. Elijah, Mingxun Wang, Clarisse Marotz, Kate E. Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J. Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H. Mills, Paulina K. Piotrowski, Stephanie L. Servetas, Sandra M. Da Silva, Christina M. Jones, Nancy J. Lin, Katrice A. Lippa, Scott A. Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S. Dulai, Tatyana I. Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M. Doty, Jae H. Kim, Kyung E. Rhee, Julia Beauchamp-Walters, Kenneth P. Wright, Maria Gloria Dominguez-Bello, Mark Manary, Michelli F. Oliveira, Brigid S. Boland, Norberto Peporine Lopes, Monica Guma, Austin D. Swafford, Rachel J. Dutton, Rob Knight, Pieter C. Dorrestein
Summary: This study introduces a reference-data-driven analysis approach to increase the usage of metabolomics MS/MS data and enable empirical evaluation of dietary patterns from untargeted data.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Erick Armingol, Hratch M. Baghdassarian, Cameron Martino, Araceli Perez-Lopez, Caitlin Aamodt, Rob Knight, Nathan E. Lewis
Summary: In this study, the authors introduce a new method called Tensor-cell2cell for deciphering context-driven intercellular communication. By considering multiple stages, states, or locations of cells, Tensor-cell2cell can uncover communication patterns associated with different phenotypic states and provide the ability to identify communication modules related to disease severity.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Camille Brewer, Tobias Lanz, Caryn R. Hale, Gregory D. Sepich-Poore, Cameron Martino, Austin D. Swafford, Thomas S. Carroll, Sarah Kongpachith, Lisa K. Blum, Serra E. Elliott, Nathalie E. Blachere, Salina Parveen, John Fak, Vicky Yao, Olga Troyanskaya, Mayu O. Frank, Michelle S. Bloom, Shaghayegh Jahanbani, Alejandro M. Gomez, Radhika Iyer, Nitya S. Ramadoss, Orr Sharpe, Sangeetha Chandrasekaran, Lindsay B. Kelmenson, Qian Wang, Heidi Wong, Holly L. Torres, Mark Wiesen, Dana T. Graves, Kevin D. Deane, V. Michael Holers, Rob Knight, Robert B. Darnell, William H. Robinson, Dana E. Orange
Summary: This study found that periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anticitrullinated protein antibodies (ACPAs), suggesting a link between oral mucosal inflammation and RA pathogenesis. The researchers also discovered that RA patients with periodontal disease experienced repeated oral bacteremias associated with transcriptional signatures of specific monocyte subsets observed in inflamed RA synovia and blood during RA flares. The bacteremia was caused by citrullinated oral bacteria and resulted in activation of ACPA B cells, promoting affinity maturation and epitope spreading to citrullinated human antigens.
SCIENCE TRANSLATIONAL MEDICINE
(2023)