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NPJ Biofilms and Microbiomes

Patrick A Rühs, Flavian Storz, Yuly A López Gómez, Matthias Haug, Peter Fischer
Bacterial cellulose is a remarkable fibrous structural component of biofilms, as it forms a mechanically strong hydrogel with high water adsorption capabilities. Additionally, bacterial cellulose is biocompatible and therefore of potential interest for skin regeneration and wound healing applications. However, bacterial cellulose produced through conventional production processes at water-air interfaces lack macroporosity control, which is crucial for regenerative tissue applications. Here we demonstrate a straightforward and efficient approach to form a macroporous bacterial cellulose foam by foaming a mannitol-based media with a bacterial suspension of Gluconoacetobacter xylinus ...
2018: NPJ Biofilms and Microbiomes
Zicheng Wang, Huazhe Lou, Ying Wang, Ron Shamir, Rui Jiang, Ting Chen
Human gut microbiomes consist of a large number of microbial genomes, which vary by diet and health conditions and from individual to individual. In the present work, we asked whether such variation or similarity could be measured and, if so, whether the results could be used for personal microbiome identification (PMI). To address this question, we herein propose a method to estimate the significance of similarity among human gut metagenomic samples based on reference-free, long k -mer features. Using these features, we find that pairwise similarities between the metagenomes of any two individuals obey a beta distribution and that a p value derived accordingly well characterizes whether two samples are from the same individual or not...
2018: NPJ Biofilms and Microbiomes
Magali de Bruyn, João Sabino, Doris Vandeputte, Séverine Vermeire, Jeroen Raes, Ghislain Opdenakker
Gut microbiota help to educate the immune system and a number of involved immune cells were recently characterized. However, specific molecular determinants in these processes are not known, and, reciprocally, little information exists about single host determinants that alter the microbiota. Gelatinase B/matrix metalloproteinase-9 (MMP-9), an innate immune regulator and effector, has been suggested as such a host determinant. In this study, acute colitis was induced in co-housed MMP-9-/- mice ( n  = 10) and their wild-type (WT) littermates ( n  = 10) via oral administration of 3% dextran sodium sulfate (DSS) for 7 days followed by 2 days of regular drinking water...
2018: NPJ Biofilms and Microbiomes
Yi Wang, Xiaojuan Tan, Chuanwu Xi, K Scott Phillips
Staphylococcus aureus ( S. aureus ) including methicillin resistant S. aureus (MRSA) is one of the primary microorganisms responsible for surgical site infection (SSI). Since S. aureus contamination is known to originate from the skin, eradicating it on the skin surface at surgical sites is an important intervention to reduce the chance of SSIs. Here we developed and evaluated the efficacy of a combination probiotic/brush sonication strategy for skin preparation at surgical, injection and insertion sites in medicine...
2018: NPJ Biofilms and Microbiomes
Héloïse Boudarel, Jean-Denis Mathias, Benoît Blaysat, Michel Grédiac
Developing reliable anti-biofilm strategies or efficient biofilm-based bioprocesses strongly depends on having a clear understanding of the mechanisms underlying biofilm development, and knowledge of the relevant mechanical parameters describing microbial biofilm behavior. Many varied mechanical testing methods are available to assess these parameters. The mechanical properties thus identified can then be used to compare protocols such as antibiotic screening. However, the lack of standardization in both mechanical testing and the associated identification methods for a given microbiological goal remains a blind spot in the biofilm community...
2018: NPJ Biofilms and Microbiomes
Salvador Gomez-Carretero, Ben Libberton, Karl Svennersten, Kristin Persson, Edwin Jager, Magnus Berggren, Mikael Rhen, Agneta Richter-Dahlfors
[This corrects the article DOI: 10.1038/s41522-017-0027-0.].
2018: NPJ Biofilms and Microbiomes
Yun Shen, Pin Chieh Huang, Conghui Huang, Peng Sun, Guillermo L Monroy, Wenjing Wu, Jie Lin, Rosa M Espinosa-Marzal, Stephen A Boppart, Wen-Tso Liu, Thanh H Nguyen
The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study...
2018: NPJ Biofilms and Microbiomes
Cassie R Bakshani, Ana L Morales-Garcia, Mike Althaus, Matthew D Wilcox, Jeffrey P Pearson, John C Bythell, J Grant Burgess
Mucus layers often provide a unique and multi-functional hydrogel interface between the epithelial cells of organisms and their external environment. Mucus has exceptional properties including elasticity, changeable rheology and an ability to self-repair by re-annealing, and is therefore an ideal medium for trapping and immobilising pathogens and serving as a barrier to microbial infection. The ability to produce a functional surface mucosa was an important evolutionary step, which evolved first in the Cnidaria, which includes corals, and the Ctenophora...
2018: NPJ Biofilms and Microbiomes
Lydia C Powell, Manon F Pritchard, Elaine L Ferguson, Kate A Powell, Shree U Patel, Phil D Rye, Stavroula-Melina Sakellakou, Niklaas J Buurma, Charles D Brilliant, Jack M Copping, Georgina E Menzies, Paul D Lewis, Katja E Hill, David W Thomas
Acquisition of a mucoid phenotype by Pseudomonas sp. in the lungs of cystic fibrosis (CF) patients, with subsequent over-production of extracellular polymeric substance (EPS), plays an important role in mediating the persistence of multi-drug resistant (MDR) infections. The ability of a low molecular weight (Mn = 3200 g mol-1 ) alginate oligomer (OligoG CF-5/20) to modify biofilm structure of mucoid Pseudomonas aeruginosa (NH57388A) was studied in vitro using scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) with Texas Red (TxRd®)-labelled OligoG and EPS histochemical staining...
2018: NPJ Biofilms and Microbiomes
Kai Bao, Nagihan Bostanci, Thomas Thurnheer, Jonas Grossmann, Witold E Wolski, Bernard Thay, Georgios N Belibasakis, Jan Oscarsson
Aggregatibacter actinomycetemcomitans is a Gram-negative organism, strongly associated with aggressive forms of periodontitis. An important virulence property of A. actinomycetemcomitans is its ability to form tenacious biofilms that can attach to abiotic as well as biotic surfaces. The histone-like (H-NS) family of nucleoid-structuring proteins act as transcriptional silencers in many Gram-negative bacteria. To evaluate the role of H-NS in A. actinomycetemcomitans , hns mutant derivatives of serotype a strain D7S were generated...
2018: NPJ Biofilms and Microbiomes
Christine Hörnlein, Veronique Confurius-Guns, Lucas J Stal, Henk Bolhuis
Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and bound nitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specific requirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique molecular timing mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about its function in a natural complex community...
2018: NPJ Biofilms and Microbiomes
Meng Pu, Dean Allistair Rowe-Magnus
Vibrio vulnificus is autochthonous to estuaries and warm coastal waters. Infection occurs via open wounds or ingestion, where its asymptomatic colonization of seafood, most infamously oysters, provides a gateway into the human food chain. Colonization begins with initial surface contact, which is often mediated by bacterial surface appendages called pili. Type IV Tad pili are widely distributed in the Vibrionaceae, but evidence for a physiological role for these structures is scant. The V. vulnificus genome codes for three distinct tad loci...
2018: NPJ Biofilms and Microbiomes
Harsh Mathur, Des Field, Mary C Rea, Paul D Cotter, Colin Hill, R Paul Ross
Biofilms are sessile communities of bacteria typically embedded in an extracellular polymeric matrix. Bacterial cells embedded in biofilms are inherently recalcitrant to antimicrobials, compared to cells existing in a planktonic state, and are notoriously difficult to eradicate once formed. Avenues to tackle biofilms thus far have largely focussed on attempting to disrupt the initial stages of biofilm formation, including adhesion and maturation of the biofilm. Such an approach is advantageous as the concentrations required to inhibit formation of biofilms are generally much lower than removing a fully established biofilm...
2018: NPJ Biofilms and Microbiomes
Alona Keren-Paz, Vlad Brumfeld, Yaara Oppenheimer-Shaanan, Ilana Kolodkin-Gal
In nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact bacterial biofilms...
2018: NPJ Biofilms and Microbiomes
Lisa Neu, Carola Bänziger, Caitlin R Proctor, Ya Zhang, Wen-Tso Liu, Frederik Hammes
Bath toys pose an interesting link between flexible plastic materials, potable water, external microbial and nutrient contamination, and potentially vulnerable end-users. Here, we characterized biofilm communities inside 19 bath toys used under real conditions. In addition, some determinants for biofilm formation were assessed, using six identical bath toys under controlled conditions with either clean water prior to bathing or dirty water after bathing. All examined bath toys revealed notable biofilms on their inner surface, with average total bacterial numbers of 5...
2018: NPJ Biofilms and Microbiomes
Gabriel Carvalho, Damien Balestrino, Christiane Forestier, Jean-Denis Mathias
Persisters form sub-populations of stress-tolerant cells that play a major role in the capacity of biofilms to survive and recover from disturbances such as antibiotic treatments. The mechanisms of persistence are diverse and influenced by environmental conditions, and persister populations are more heterogeneous than formerly suspected. We used computational modeling to assess the impact of three switching strategies between susceptible and persister cells on the capacity of bacterial biofilms to grow, survive and recover from antibiotic treatments...
2018: NPJ Biofilms and Microbiomes
Elio Emilio Gonzo, Stefan Wuertz, Veronica B Rajal
Biofilm systems can be modeled using a variety of analytical and numerical approaches, usually by making simplifying assumptions regarding biofilm heterogeneity and activity as well as effective diffusivity. Inhibition kinetics, albeit common in experimental systems, are rarely considered and analytical approaches are either lacking or consider effective diffusivity of the substrate and the biofilm density to remain constant. To address this obvious knowledge gap an analytical procedure to estimate the effectiveness factor (dimensionless substrate mass flux at the biofilm-fluid interface) was developed for a continuum heterogeneous biofilm with multiple limiting-substrate Monod kinetics to different types of inhibition kinetics...
2018: NPJ Biofilms and Microbiomes
Caitlin N Spaulding, Roger D Klein, Henry L Schreiber, James W Janetka, Scott J Hultgren
The emergence of drug-resistant pathogens has led to a decline in the efficacy of traditional antimicrobial therapy. The rise in resistance has been driven by widespread use, and in some cases misuse, of antibacterial agents in treating a variety of infections. A growing body of research has begun to elucidate the harmful effects of broad-spectrum antibiotic therapy on the beneficial host microbiota. To combat these threats, increasing effort is being directed toward the development of precision antimicrobial therapeutics that target key virulence determinants of specific pathogens while leaving the remainder of the host microbiota undisturbed...
2018: NPJ Biofilms and Microbiomes
Majken Sønderholm, Klaus Koren, Daniel Wangpraseurt, Peter Østrup Jensen, Mette Kolpen, Kasper Nørskov Kragh, Thomas Bjarnsholt, Michael Kühl
In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate bead model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers...
2018: NPJ Biofilms and Microbiomes
Fabien Cottier, Kandhadayar Gopalan Srinivasan, Marina Yurieva, Webber Liao, Michael Poidinger, Francesca Zolezzi, Norman Pavelka
Sequencing-based microbiome profiling aims at detecting and quantifying individual members of a microbial community in a culture-independent manner. While amplicon-based sequencing (ABS) of bacterial or fungal ribosomal DNA is the most widely used technology due to its low cost, it suffers from PCR amplification biases that hinder accurate representation of microbial population structures. Shotgun metagenomics (SMG) conversely allows unbiased microbiome profiling but requires high sequencing depth. Here we report the development of a meta-total RNA sequencing (MeTRS) method based on shotgun sequencing of total RNA and benchmark it on a human stool sample spiked in with known abundances of bacterial and fungal cells...
2018: NPJ Biofilms and Microbiomes
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