Article
Critical Care Medicine
Heather D. Green, Andrew M. Jones
Summary: Cystic fibrosis is a disease characterized by chronic airway infection and progressive decline in respiratory function. Recent changes in the landscape of airway infection in CF have resulted in an increased prevalence of atypical gram-negative bacterial infections. The clinical relevance and treatment strategies for many of these lower prevalence organisms are still not well understood.
Article
Biotechnology & Applied Microbiology
Jiacheng Chuan, Anatoly Belov, Michel Cloutier, Xiang Li, Izhar U. H. Khan, Wen Chen
Summary: This study conducted comparative genomics analysis and PCR assays to identify the virulence, antibiotic-resistance, and toxin genes in the genomes of A. faecis and A. lanthieri reference strains. The results highlighted the potential zoonotic pathogenicity of these two species, but further studies are needed to explore genetic variations in virulence-related genes among different strains and assess their potential as opportunistic pathogens for animals and humans.
Article
Infectious Diseases
Ana C. Blanchard, Valerie J. Waters
Summary: Cystic fibrosis (CF) is a common genetic disease in Caucasians, leading to respiratory failure caused by chronic infections. The respiratory infections in CF patients are caused by opportunistic pathogens such as Pseudomonas aeruginosa, Burkholderia spp., Achromobacter spp., Stenotrophomonas maltophilia, anaerobes, nontuberculous mycobacteria, and fungi. Culture-independent methods have revealed the polymicrobial nature and dynamics of microbial communities in CF lung infections. The unique environment of the CF airway facilitates infections by opportunistic pathogens. Infectious disease physicians should be aware of the differences in epidemiology and disease role of these pathogens in CF compared to other medical conditions.
JOURNAL OF THE PEDIATRIC INFECTIOUS DISEASES SOCIETY
(2022)
Article
Biotechnology & Applied Microbiology
Ingrid E. Meyer Cifuentes, Julius Degenhardt, Meina Neumann-Schaal, Nico Jehmlich, David Kamanda Ngugi, Basak Oeztuerk
Summary: This study investigates the degradation of biodegradable plastics in the aquatic environment and demonstrates the role of microbial communities in this process. The researchers found that the type of polymer determines the community structure and degradation capability, with different polymers resulting in different levels of diversity and degradation activity. The study also identified three enzymes capable of degrading a range of biodegradable polymers, which could have potential biotechnological applications.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Shuangfei Zhang, Charles Amanze, Chongran Sun, Kai Zou, Shaodong Fu, Yan Deng, Xueduan Liu, Yili Liang
Summary: In this study, two novel xenobiotics-degrading strains affiliated with Azonexaceae were isolated and proposed as a new species within Dechloromonas based on genomic and multi-phylogenetic analysis. These strains play a role in the cometabolic process of some xenobiotics in natural communities and possess diverse metabolic capabilities such as nitrogen metabolism and biodegradation of various xenobiotics. Members of this novel species were found globally in different environments, indicating a potential role in the biodegradation of xenobiotics.
Article
Multidisciplinary Sciences
Rui-Fang Gao, Ying Wang, Ying Wang, Zhi-Wen Wang, Gui-Ming Zhang
Summary: In this study, we identified Pandoraea sp. 892iso as Pandoraea sputorum through genome identification and comparative genomic analysis. Additionally, we speculated that Pandoraea sp. 892iso is an endosymbiont of Phytophthora rubi.
Article
Genetics & Heredity
Ma. Angeles Cabrera, Sebastian L. Marquez, Jose M. Perez-Donoso
Summary: This study investigated the TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica. Comparative genomic analysis revealed that these isolates have a high abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. They also possess unique genes involved in TNT transformation and the beta-ketoadipate pathway for aromatic compound degradation.
Review
Cell Biology
Francesca Saluzzo, Luca Riberi, Barbara Messore, Nicola Ivan Lore, Irene Esposito, Elisabetta Bignamini, Virginia De Rose
Summary: Cystic Fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene, leading to imbalances in the airway microenvironment and increased susceptibility to infections. CFTR modulators have shown promise in improving airway infections, but their long-term effects remain to be fully understood.
Review
Infectious Diseases
Viola Camilla Scoffone, Gabriele Trespidi, Giulia Barbieri, Samuele Irudal, Elena Perrin, Silvia Buroni
Summary: This review summarizes the principal RND efflux pump families described in CF pathogens, with a focus on the main Gram-negative bacterial species, where RND pumps have been associated with MDR phenotypes.
Article
Endocrinology & Metabolism
F. Patane, G. Pecora, A. Giallongo, S. Manti, E. Gitto, G. Antonio, C. Cuppari, G. Ceravolo, R. Chimenz, G. F. Parisi, M. Papale, N. Rotolo, E. Mule, S. Leonardi
Summary: Fungi and non-tuberculous mycobacteria (NTM) are increasingly found in the sputum of cystic fibrosis (CF) patients, posing diagnostic and therapeutic challenges for clinicians. Therefore, it is crucial to implement screening programs for these pathogens in all CF patients, especially those experiencing unexplained worsening of lung function. Infections caused by these pathogens also contribute significantly to morbidity and mortality in the post-transplant period. Early diagnosis and treatment are essential for managing all CF patients.
JOURNAL OF BIOLOGICAL REGULATORS AND HOMEOSTATIC AGENTS
(2022)
Article
Infectious Diseases
Zhiyi Ma, Xin Zou, Jinhao Lin, Chunchun Zhang, Shuhua Xiao
Summary: This case report describes a non-cystic fibrosis female who developed sepsis due to P. sputorum infection, which was successfully treated with a two-month course of intravenous antibiotics and comprehensive care. Susceptibility testing showed resistance to several antibiotics but sensitivity to imipenem, highlighting the potential virulence of Pandoraea species and the importance of early identification for appropriate treatment strategies.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Pediatrics
Patricia M. Lenhart-Pendergrass, Meg Anthony, Sabina Sariyska, Ashley Andrews, Heather Scavezze, Elinor Towler, Stacey L. Martiniano, Jordana E. Hoppe, Edith T. Zemanick
Summary: Home collection of oropharyngeal swabs for bacterial culture is feasible in children with cystic fibrosis across a range of ages. The majority of home-collected specimens showed growth of one or more cystic fibrosis pathogens, with results comparable to recent in-clinic specimens.
PEDIATRIC PULMONOLOGY
(2021)
Article
Microbiology
Zaki Saati-Santamaria, Riccardo Baroncelli, Raul Rivas, Paula Garcia-Fraile
Summary: Each Earth ecosystem has unique microbial communities, and Pseudomonas bacteria have evolved to adapt to different ecological niches and interact with different hosts. This study revealed the functional divergence of Pseudomonas depending on the niche, with each group of strains from a certain environment harboring distinct metabolic pathways or functions. Horizontal gene transfer was found to occur mainly between closely related taxa and was dependent on the isolation source. Additionally, numerous undescribed proteins and functions associated with each Pseudomonas lifestyle were discovered.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Rosa Bellavita, Angela Maione, Simone Braccia, Marica Sinoca, Stefania Galdiero, Emilia Galdiero, Annarita Falanga
Summary: Chronic lung infections in CF patients are caused by multidrug-resistant bacteria. Traditional antibiotics are ineffective in treating these infections, highlighting the need for novel molecules. Antimicrobial peptides (AMPs) show promise due to their antimicrobial, anti-inflammatory, and immunomodulatory activities. A more stable version of the peptide WMR (WMR-4) was developed and studied for its ability to inhibit and eradicate biofilms in CF patients in vitro and in vivo.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Infectious Diseases
Lucie Peyclit, Sophie Alexandra Baron, Martine Reynaud-Gaubert, Nadim Cassir, Jean-Marc Rolain
Summary: A 26-year-old female with longstanding colonization by Pandoraea nosoerga underwent liver-lung transplantation for cystic fibrosis in 2018, and developed post-transplant bacteremic pneumonia caused by extensively drug-resistant P. nosoerga. Drug repurposing was used for treatment optimization. Comparative whole-genome sequencing revealed that post-transplant contamination was from her own pre-transplant strain, highlighting the importance of effective decontamination protocols before transplantation.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Microbiology
Bram Danneels, Monique Blignaut, Guillaume Marti, Simon Sieber, Peter Vandamme, Marion Meyer, Aurelien Carlier
Summary: The symbiotic relationships between plants of the Rubiaceae and Primulaceae families and Burkholderia bacteria are unique and intimate. This study assembled and analyzed 17 new endophyte genomes, revealing that all endophytes, despite their taxonomic diversity, contained gene clusters linked to the production of specialized metabolites. Acquisition of secondary metabolite gene clusters through horizontal gene transfer is proposed to be a prerequisite for the evolution of a stable association between these endophytes and their hosts.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Margo Olbrecht, Fedoua Echahidi, Denis Pierard, Charlotte Peeters, Peter Vandamme, Ingrid Wybo, Thomas Demuyser
Summary: We conducted in vitro antimicrobial susceptibility testing of 267 Achromobacter isolates for 16 antibiotics from 2017 to 2022. The highest susceptibility was found for piperacillin-tazobactam (70%) and ceftazidime-avibactam (62%). Between 30% and 49% of strains were susceptible to tigecycline, ceftazidime, and meropenem. We applied species-specific Achromobacter xylosoxidans breakpoints for piperacillin-tazobactam, meropenem, and trimethoprim-sulfamethoxazole and EUCAST pharmacokinetic/pharmacodynamic (PK/PD) breakpoints for the others. A. xylosoxidans was the most frequently isolated species, followed by Achromobacter insuavis and Achromobacter ruhlandii.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Amanda Hettiarachchi, Margo Cnockaert, Marie Joossens, David Laureys, Jessika De Clippeleer, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, Dirk C. de Graaf, Peter Vandamme
Summary: This study analyzed the cultivable bacterial communities of different compartments in the invasive insect Vespa velutina, as well as the nest samples, using both cultivation and 16S rRNA amplicon sequencing. The bacterial symbionts in Vespa velutina were dominated by Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas, and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum were generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus were highly specialized core LAB symbionts with reduced genome sizes. Sphingomonas and Spiroplasma were non-LAB core symbionts, but they were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted to amino acid metabolism, and Convivina praedatoris sp. nov., which was adapted to carbohydrate metabolism.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tina Tuerlings, Amanda Hettiarachchi, Marie Joossens, Benoit Geslin, Nicolas J. J. Vereecken, Denis Michez, Guy Smagghe, Peter Vandamme
Summary: The study characterized the gut microbiota of invasive bee Megachile sculpturalis from native and invaded regions. The microbiota communities in bees from invaded regions were similar and different from those in Japan. Core amplicon sequence variants (ASVs) represented micro-organisms commonly present in bee-associated niches. The absence of known bee pathogens and presence of microparasite infections suggest a potential role of pathogen pressure and natural enemies in the invasion success of M. sculpturalis.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Food Science & Technology
Louise Vermote, Jonas De Roos, Margo Cnockaert, Peter Vandamme, Stefan Weckx, Luc De Vuyst
Summary: Belgian lambic beers are produced using traditional craftsmanship, relying on wooden barrels for spontaneous fermentation and maturation. These barrels play a crucial role in establishing a stable microbial ecosystem, minimizing batch-to-batch variations, and preventing flavor deviations. They provide an inoculation source of necessary microorganisms and a microaerobic environment for successful lambic beer production.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Microbiology
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kaempfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon- Wo Kwon
Summary: In this study, two strains of bacteria were isolated from wasps in Germany and Korea. Molecular and phenotypic analysis showed that these strains are closely related to known species but also have distinct characteristics. Therefore, it is proposed to name these strains Aristophania vespae.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Peter Vandamme, Charlotte Peeters, Amanda Hettiarachchi, Margo Cnockaert, Aurelien Carlier
Summary: Strain LMG 31809 T was isolated from a top soil sample in Belgium and classified as a rare biosphere bacterium that occurs at low abundances in multiple soil and water ecosystems. It represents a new species within a new genus, Govania unica gen. nov., sp. nov, belonging to the class Alphaproteobacteria. The strain is strictly aerobic and uses organic acids and possibly aromatic compounds as growth substrates. Its whole-genome sequence has a size of 3.21 Mbp with a G + C content of 58.99 mol%.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Nanzhen Qiao, Julia Bechtner, Margo Cnockaert, Eliza Depoorter, Christian Diaz-Munoz, Peter Vandamme, Luc De Vuyst, Michael G. Ganzle
Summary: This study characterized the genus Periweissella through phylogenetic analysis and genomic analysis, revealing its evolutionary relationship with closely related genera Weissella and Furfurilactobacillus. The study also determined the genetic and physiological traits of the genus. Results showed that Periweissella is the link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade, and it is the only heterofermentative genus in the Lactobacillaceae that comprises predominantly motile strains.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Amanda Hettiarachchi, Margo Cnockaert, Marie Joossens, Antoine Gekiere, Ivan Meeus, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, Peter Vandamme
Summary: We characterized the microbial communities in different parts of four wild solitary bee species and found that the dominant bacteria were endosymbionts such as Wolbachia and Spiroplasma. Other bacterial and yeast genera were associated with environmental sources. The bacterial communities varied between bee species, gut compartments, and ovaries, suggesting a selective process influenced by floral and host traits. Many of the gut symbionts identified in this study exhibited metabolic versatility.
Article
Biotechnology & Applied Microbiology
Atena Sadat Sombolestani, Dries Bongaerts, Eliza Depoorter, Ilse Cleenwerck, Anneleen D. Wieme, Scott J. Britton, Stefan Weckx, Luc De Vuyst, Peter Vandamme
Summary: Polyphasic taxonomic and comparative genomic analyses revealed a novel species among acetic acid bacteria, named Brytella acorum gen. nov., sp. nov., represented by lambic beer isolates including strain LMG 32668T and the kombucha isolate LMG 32879. This species has Acidomonas methanolica as its closest phylogenomic neighbor and possesses metabolic characteristics typical of acetic acid bacteria. The absence of glycolysis pathway and the presence of both aerobic respiration and oxidative fermentation for energy metabolism are notable features. Antibiotic resistance genes and virulence factors are absent.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Biology
Luc Cornet, Benoit Durieu, Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Valerian Lupo, Ilse Cleenwerck, Heide-Marie Daniel, Leen Rigouts, Damien Sirjacobs, Stephane Declerck, Peter Vandamme, Annick Wilmotte, Denis Baurain, Pierre Becker
Summary: A bioinformatics toolbox called GEN-ERA has been developed by the Belgian Coordinated Collections of Microorganisms. It allows researchers to perform robust phylogenomic analyses on bacteria and small eukaryotes without specific training in bioinformatics. The toolbox provides workflows for genome downloading, quality assessment, contamination estimation, tree reconstruction, average nucleotide identity comparisons, and metabolic modeling. It has been tested on various microorganisms and used in a case study on Gloeobacterales for microbial taxonomy.
Article
Microbiology
Juliana Botero, Atena Sadat Sombolestani, Margo Cnockaert, Charlotte Peeters, Wim Borremans, Luc De Vuyst, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, German Bonilla-Rosso, Philipp Engel, Peter Vandamme
Summary: This study provides insights into the diversity and function of Commensalibacter bacteria in various insect species. Through analysis of their whole-genome sequences, it was found that Commensalibacter strains can be classified into four species, which share similar genetic pathways for central metabolism. However, there are differences in genome size, G+C content, amino acid metabolism, and carbohydrate-utilizing enzymes among these species. Notably, the study on the Western honey bee symbiont, C. melissae, revealed its unique characteristics such as reduced genome size and a large number of species-specific gene clusters.
Article
Environmental Sciences
Leon Marshall, Nicolas Leclercq, Timothy Weekers, Insafe El Abdouni, Luisa G. Carvalheiro, Michael Kuhlmann, Denis Michez, Pierre Rasmont, Stuart P. M. Roberts, Guy Smagghe, Peter Vandamme, Thomas Wood, Nicolas J. Vereecken
Summary: Visitation by wild bee species is essential for apple production, but they are vulnerable to climate change. We modeled the distribution range shifts of key apple-pollinating bee species under different climate change scenarios and found that overall contractions in range are limited. However, under the worst-case scenario, some countries such as France and Italy may experience significant loss in bee populations and potential pollination services. Climate change is not the only threat to apple pollination, and future deficits will also depend on orchard management and ecological infrastructure.
GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS
(2023)
