Article
Environmental Sciences
B. Reyneke, M. Waso, T. Ndlovu, T. Clements, B. Havenga, S. Khan, W. Khan
Summary: This study compared the effectiveness of EMA and PMA combined with ABS and qPCR assays in detecting viable bacterial species in rainwater. The results showed that both EMA and PMA reduced the detection of nonviable bacteria in rainwater samples, but EMA treatment significantly altered the relative abundance of dominant bacterial families and genera, as well as decreased the detection of unclassified bacteria. Additionally, the use of EMA and PMA increased the detection of less abundant pathogenic bacteria. The combination of viability pre-treatments with ABS and qPCR provides a comprehensive monitoring approach for detecting less abundant bacterial genera and/or pathogens in water sources.
WATER AIR AND SOIL POLLUTION
(2022)
Article
Soil Science
Xiaojing Hu, Zhongjun Jia, Junjie Liu, Haidong Gu, Baoku Zhou, Dan Wei, Jian Jin, Xiaobing Liu, Guanghua Wang
Summary: Archived soils are valuable for microbial ecological research and can be used to reanalyze published data. However, few studies have examined the effects of prolonged archived soil on microbial communities. This study sequenced archived fertilized soils and frozen soils stored for 7 years, and found that prolonged desiccation significantly impacted bacterial diversity and community structure. Removal of relic DNA improved the accuracy of diversity and reduced differences between archived and frozen soils. The findings suggest that desiccation effects can be improved by removing relic DNA and archived soils can still be used for microbial ecology research.
SOIL & TILLAGE RESEARCH
(2023)
Article
Microbiology
Thomas H. Hampton, Devin Thomas, Christopher van der Gast, George A. O'Toole, Bruce A. Stanton
Summary: This study identified five bacterial community types in CF patients, explaining 24% of lung function variability and suggesting that community stability is associated with a risk of lung function decline. Patients with severe disease experienced more shifts among community types, emphasizing the importance of understanding factors that drive shifts in community composition.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Ya Wang, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Summary: This study comprehensively evaluates PMA-seq in synthetic and complex microbial communities, finding that the technique is effective for semi-quantitative purposes in simple synthetic communities but provides only qualitative assessments in realistically complex community samples.
Article
Microbiology
Clemence Loublier, Bernard Taminiau, Julia Heinen, Laureline Lecoq, Helene Amory, Georges Daube, Carla Cesarini
Summary: This in vitro study aimed to assess the effect of a commonly used pre-FMT processing method on the bacterial composition and viability of the fecal filtrate. The results showed that the major bacterial populations in equine feces remained viable when using the described pre-FMT protocol, but the relative abundances of some minor genera were significantly different in the final filtrate.
Review
Microbiology
Francesca Bugli, Cecilia Martini, Maura Di Vito, Margherita Cacaci, Daniele Catalucci, Alessandro Gori, Michele Iafisco, Maurizio Sanguinetti, Alberto Vitali
Summary: Antibiotic resistance is a major global health and social issue that will have significant repercussions on world health and the economy in the near future. To address this, researchers in medical, microbiological, and biochemical fields are exploring the potential of antimicrobial peptides (AMPs) as an alternative to conventional drugs. This review focuses on the application of AMPs in the specific context of cystic fibrosis (CF), highlighting different types of natural, naturally modified, and synthetic peptides, as well as strategies to overcome barriers and adapt to physiological conditions.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Engineering, Environmental
Wenhao Liu, Peng Xiang, Yuan Ji, Zeyou Chen, Zhongfang Lei, Weiwei Huang, Wenli Huang, Dongfang Liu
Summary: This study quantified the presence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in viable and dead bacteria using the propidium monoazide (PMA) shielding method. The results showed that viable bacteria carried a significant proportion of ARGs and MGEs, providing important insights into the actual AMR risk and viable hosts. This research is crucial for understanding and controlling AMR in wastewater treatment plants.
Article
Medicine, General & Internal
Anna Engell Holm, Hans Henrik Lawaetz Schultz, Helle Krogh Johansen, Tania Pressler, Thomas Kromann Lund, Martin Iversen, Michael Perch
Summary: This study monitored the time of bacterial re-colonization in lung transplant patients with cystic fibrosis and found that 70% of patients were re-colonized by bacteria after 2 years, with no observed impact on survival rates from re-colonization or different bacterial species.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Environmental Sciences
Jun Yang, Kui Huang, Lansheng Peng, Jianhui Li, Aozhan Liu
Summary: The study showed that earthworms have a significant impact on the functional microbial communities in sludge, accelerating the decomposition of organic matter. Compared to the control group, the diversity of active bacteria and eukaryotes decreased in vermicomposting, forming a specific-functional microbial community.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Respiratory System
Christina S. Thornton, Lisa A. Carmody, Linda M. Kalikin, Kristopher Opron, Lindsay J. Caverly, John J. Lipuma
Summary: In people with cystic fibrosis and advanced lung disease, a considerable proportion do not have low-diversity airway bacterial communities characterized by a dominant genus, and these individuals have better survival outcomes. The absence of a dominant genus, presence of methicillin-susceptible Staphylococcus aureus, and greater bacterial richness are positively correlated with lung function, while higher relative abundance of the dominant genus and greater antimicrobial use are negatively correlated with lung function. These findings suggest potential avenues for improved management strategies in these patients.
JOURNAL OF CYSTIC FIBROSIS
(2023)
Review
Microbiology
Jim Manos
Summary: The aim of antimicrobial treatment for bacterial infections in CF lung is to improve infection outcomes for patients. Current treatments include antibiotics with physical therapy, but there are challenges such as bacterial survival in biofilm aggregates. Emerging treatments involving novel compounds or bacteriophages show promise in disrupting biofilm matrix and improving antibiotic access.
Article
Respiratory System
Mette Kolpen, Kasper Norskov Kragh, Juan Barraza Enciso, Daniel Faurholt-Jepsen, Birgitte Lindegaard, Gertrud Baunbaek Egelund, Andreas Vestergaard Jensen, Pernille Ravn, Inger Hee Mabuza Mathiesen, Alexandra Gabriella Gheorge, Frederik Boetius Hertz, Tavs Qvist, Marvin Whiteley, Peter Ostrup Jensen, Thomas Bjarnsholt
Summary: This study found that both acute and chronic lung infections are dominated by biofilms, and bacteria grew faster in sputum from acute infections, but these fast-growing bacteria were also enriched in biofilms similar to chronic infections. Cellular inflammation in the lungs was similar across patient groups, but systemic inflammatory markers were only elevated in acute infections.
Review
Immunology
Mario Cocorullo, Laurent R. Chiarelli, Giovanni Stelitano
Summary: Reverse vaccinology is a powerful tool used to develop vaccines from a pathogen genome. It is especially important for individuals with chronic pulmonary diseases, such as Cystic Fibrosis, to have effective vaccines for various bacterial infections. The approach of developing a broad-spectrum vaccine using conserved proteins across different species through computational analysis of microbial genomes has shown promising progress.
Review
Microbiology
Eneko Santos-Fernandez, Leire Martin-Souto, Aitziber Antoran, Maialen Areitio, Leire Aparicio-Fernandez, Jean-Philippe Bouchara, Carsten Schwarz, Aitor Rementeria, Idoia Buldain, Andoni Ramirez-Garcia
Summary: This review article discusses the interactions between fungi and bacteria in the respiratory tract of cystic fibrosis patients and their potential effects on the disease. It highlights the various molecules involved, such as quorum sensing-regulated molecules and fungal compounds, and their role in colonization, inflammation, and infection. Despite competition between microorganisms, co-colonization rates suggest that multiple factors influence the interactions. Therefore, further scientific and economic efforts are needed to intensify studies on bacterial-fungal inter-kingdom interactions in cystic fibrosis.
FEMS MICROBIOLOGY REVIEWS
(2023)
Review
Infectious Diseases
Jaideep Vazirani, Thomas Crowhurst, C. Orla Morrissey, Gregory Snell
Summary: Cystic fibrosis is a genetic multisystem disease, and lung transplantation is an effective treatment option. However, managing recurrent infections and balancing immune suppression in this setting can be difficult. Infections are a major contributor to post-transplant mortality, with multidrug-resistant organisms posing a significant threat to survival.
INFECTION AND DRUG RESISTANCE
(2021)
Article
Nutrition & Dietetics
Kerry L. Ivey, Xuan-Mai T. Nguyen, Deirdre K. Tobias, Rebecca Song, Geraint B. Rogers, Yuk-Lam Ho, Ruifeng Li, Peter W. F. Wilson, Kelly Cho, J. Michael Gaziano, Walter C. Willett, Luc Djousse
Summary: This study found that yogurt consumption was positively associated with high-density lipoprotein cholesterol (HDLC) and negatively associated with triglyceride concentrations, which was distinct from non-yogurt dairy foods.
CLINICAL NUTRITION ESPEN
(2021)
Article
Respiratory System
Charlotte Rigauts, Juliana Aizawa, Steven L. Taylor, Geraint B. Rogers, Matthias Govaerts, Paul Cos, Lisa Ostyn, Sarah Sims, Eva Vandeplassche, Mozes Sze, Yves Dondelinger, Lars Vereecke, Heleen Van Acker, Jodie L. Simpson, Lucy Burr, Anne Willems, Michael M. Tunney, Cristina Cigana, Alessandra Bragonzi, Tom Coenye, Aurelie Crabbe
Summary: The presence of Rothia mucilaginosa in the lower airways has an inhibitory effect on pathogen-induced inflammation and is negatively correlated with pro-inflammatory markers in bronchiectasis patients. Mechanistically, R. mucilaginosa inhibits inflammation by reducing NF-kappa B pathway activation. These findings suggest that R. mucilaginosa in the lower airways could potentially mitigate inflammation and impact the severity and progression of chronic respiratory disorders.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Meeting Abstract
Nutrition & Dietetics
S. Shallangwa, P. J. Morgan, A. W. Walker, A. W. Ross
PROCEEDINGS OF THE NUTRITION SOCIETY
(2022)
Article
Genetics & Heredity
Paul O. Sheridan, Petra Louis, Eleni Tsompanidou, Sophie Shaw, Hermie J. Harmsen, Sylvia H. Duncan, Harry J. Flint, Alan W. Walker
Summary: Lactate accumulation in the human gut is related to negative health impacts, but lactate can be consumed and converted to beneficial short-chain fatty acids by lactate-utilizing bacteria. Transcriptomic analyses of two species of lactate-utilizing bacteria revealed differences in gene expression, potentially related to their ecological niches in the gut.
MICROBIAL GENOMICS
(2022)
Review
Biochemistry & Molecular Biology
Andrew P. Shoubridge, Jocelyn M. Choo, Alyce M. Martin, Damien J. Keating, Ma-Li Wong, Julio Licinio, Geraint B. Rogers
Summary: The gut microbiome has a significant influence on human neurophysiology and mental health, playing a role in the development of psychiatric conditions and the effectiveness of common therapies. With an increasing acceptance of its role, research is now shifting towards using this knowledge to improve clinical outcomes and understanding the mechanisms of gut microbiome-brain interactions.
MOLECULAR PSYCHIATRY
(2022)
Article
Microbiology
Natalia Molinero, Elena Conti, Alan W. Walker, Abelardo Margolles, Sylvia H. Duncan, Susana Delgado
Summary: This study presents unique insights into metabolic interactions between two bacterial isolates, Ruminococcus gauvreauii IPLA60001 and Ruminococcoides bili IPLA60002, from human gallbladder. The strains showed resistance to bile and differed in carbohydrate metabolism, amino acid catabolism, and vitamin synthesis capabilities. Transcriptomic analysis revealed their synergistic interactions, providing evidence for syntrophic metabolic cooperation between bacterial strains isolated from human bile.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Umer Zeeshan Ijaz, Ozan Gundogdu, Ciara Keating, Miriam van Eekert, Walter Gibson, Julian Parkhill, Faraji Abilahi, Benard Liseki, Viet-Anh Nguyen, Steven Sudgen, Christopher Quince, Jeroen H. J. Ensink, Belen Torondel, Alan W. Walker
Summary: This study conducted a spatial analysis of 35 Tanzanian pit latrines to investigate the bacteria and environmental factors associated with fill-up rates. The research found a linear gradient of beta diversity with increasing pit latrine sample depth, indicating a shift in microbial community structure. Factors such as pH, volatile solids, volatile fatty acids, and phosphate were identified as strongly correlated with fill-up rates. The study enhances understanding of the microbiota within pit latrines and provides new insights for future research on the decomposition process.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Katherine M. Kennedy, Marcus C. de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Backhed, Peer Bork, Thorsten Braun, Frederic D. Bushman, Joel Dore, Willem M. de Vos, Ashlee M. Earl, Jonathan A. Eisen, Michal A. Elovitz, Stephanie C. Ganal-Vonarburg, Michael G. Ganzle, Wendy S. Garrett, Lindsay J. Hall, Mathias W. Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J. Macpherson, Ruth C. Massey, Alice Carolyn McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O'Mahony, Paul W. O'Toole, Eric G. Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M. Sloboda, Gordon C. S. Smith, Harry Sokol, Tim D. Spector, Michael G. Surette, Gerald W. Tannock, Alan W. Walker, Moran Yassour, Jens Walter
Summary: The colonization of microbial communities in the human fetus and the prenatal intrauterine environment is still controversial. Recent studies analyzing microbial populations in human fetuses indicate that the detected signals might be due to contamination during sample collection or DNA sequencing processes. The presence of live and replicating microbial populations in healthy fetal tissues contradicts fundamental concepts in immunology and clinical microbiology. This has significant implications for our understanding of human immune development and highlights the challenges in studying microbial communities in low-biomass environments.
Editorial Material
Nutrition & Dietetics
Benjamin Momo Kadia, Mary Iwaret Otiti, Anouschka S. Ramsteijn, Doudou Sow, Babacar Faye, Claire Heffernan, Lindsay J. Hall, Joanne P. Webster, Alan W. Walker, Stephen Allen
Summary: In children exposed to poor hygiene and sanitation, invasion of the gut by pathogenic microbes may lead to a subclinical enteropathy known as environmental enteric dysfunction (EED), causing undernutrition, growth faltering, and impaired organ development. EED may already be present in early infancy, thus interventions that can be initiated early in life along with breastfeeding are necessary to prevent or alleviate EED. Dietary supplementation with pro-, pre-, or synbiotics could be a practical and safe approach for enhancing the resilience of the developing gut microbiota against adverse environmental factors, thereby preventing EED.
Review
Biochemistry & Molecular Biology
Sylvia H. Duncan, Elena Conti, Liviana Ricci, Alan W. Walker
Summary: A dense microbial community resides in the human colon, with considerable inter-individual variability in composition. The composition of the microbiota can be influenced by dietary complex carbohydrates and the consumption of diets high in animal protein and fat. The metabolic outputs of colonic microbes are derived from complex networks of microbial metabolic pathways and interactions, which are still not fully understood.
Article
Nutrition & Dietetics
Teresa Grohmann, Alan W. Walker, Wendy R. Russell, Nigel Hoggard, Xuguang Zhang, Graham Horgan, Baukje de Roos
Summary: Supplementation with bilberry and grape seed extract for 12 weeks improved blood pressure in individuals at risk of type 2 diabetes, but had no effect on blood sugar or cholesterol. Responders to the supplementation had specific bacterial strains and ability to metabolize catechin into smaller phenolic compounds.
FRONTIERS IN NUTRITION
(2023)
Review
Microbiology
Alan W. W. Walker, Lesley Hoyles
Summary: Interest in human microbiome research has grown significantly in the past two decades, but with it comes hype and misinformation that can undermine progress and public trust. This article highlights myths and misconceptions in the literature, emphasizing the importance of evidence-based research and recognizing the complexity of the human microbiome.
NATURE MICROBIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Margot Delavy, Natacha Sertour, Etienne Patin, Emmanuelle Le Chatelier, Nathaniel Cole, Florian Dubois, Zixuan Xie, Violaine Saint-Andre, Chaysavanh Manichanh, Alan W. Walker, Lluis Quintana-Murci, Darragh Duffy, Christophe d'Enfert, Marie-Elisabeth Bougnoux
Summary: This study investigated the host factors that influence the colonization of Candida albicans in the gut. It found that gut microbiota composition, lifestyle factors including diet, and genetics could shape the intestinal carriage of C. albicans. Additionally, the study showed that the levels of C. albicans in the intestine might influence the host immune response. These findings provide potential new strategies to control C. albicans intestinal overgrowth.
Article
Microbiology
Rebecca H. Smith, Laura Glendinning, Alan W. Walker, Mick Watson
Summary: This study emphasizes the importance of accurate reference databases in taxonomic classification of metagenomic data. The choice and composition of reference databases significantly affect classification results and accuracy, and the NCBI RefSeq database was found to be unreliable. Adding cultured reference genomes and metagenome-assembled genomes (MAGs) can greatly improve classification accuracy, especially in understudied environments. However, the accuracy of classification is strongly dependent on the taxonomic labels assigned to these genomes.
Article
Microbiology
Liviana Ricci, Joanna Mackie, Gillian E. Donachie, Ambre Chapuis, Kristyna Mezerova, Megan D. Lenardon, Alistair J. P. Brown, Sylvia H. Duncan, Alan W. Walker
Summary: This study found variations in the ability of gut microbiota to inhibit the fungal pathogen Candida albicans. Bifidobacteria and their fermentation acids were identified as important components in inhibitory gut microbiota. The findings provide insights into the potential mechanisms of gut microbiome-mediated colonization resistance against Candida albicans and suggest bifidobacteria and fermentation acids as targets for further study.
FEMS MICROBIOLOGY ECOLOGY
(2022)