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NPJ Biofilms and Microbiomes

Zicheng Wang, Huazhe Lou, Ying Wang, Ron Shamir, Rui Jiang, Ting Chen
[This corrects the article DOI: 10.1038/s41522-018-0065-2.].
2018: NPJ Biofilms and Microbiomes
Haris Antypas, Ferdinand X Choong, Ben Libberton, Annelie Brauner, Agneta Richter-Dahlfors
The ability of uropathogenic Escherichia coli (UPEC) to adopt a biofilm lifestyle in the urinary tract is suggested as one cause of recurrent urinary tract infections (UTIs). A clinical role of UPEC biofilm is further supported by the presence of bacterial aggregates in urine of UTI patients. Yet, no diagnostics exist to differentiate between the planktonic and biofilm lifestyle of bacteria. Here, we developed a rapid diagnostic assay for biofilm-related UTI, based on the detection of cellulose in urine. Cellulose, a component of biofilm extracellular matrix, is detected by a luminescent-conjugated oligothiophene, which emits a conformation-dependent fluorescence spectrum when bound to a target molecule...
2018: NPJ Biofilms and Microbiomes
Peter P Sun, Elbashir M Araud, Conghui Huang, Yun Shen, Guillermo L Monroy, Shengyun Zhong, Zikang Tong, Stephen A Boppart, J Gary Eden, Thanh H Nguyen
Biofilms exist and thrive within drinking water distribution networks, and can present human health concerns. Exposure of simulated drinking water biofilms, grown from groundwater, to a 9 × 9 array of microchannel plasma jets has the effect of severely eroding the biofilm and deactivating the organisms they harbor. In-situ measurements of biofilm structure and thickness with an optical coherence tomography (OCT) system show the biofilm thickness to fall from 122 ± 17 µm to 55 ± 13 µm after 15 min...
2018: NPJ Biofilms and Microbiomes
Ana E Duran-Pinedo, Jose Solbiati, Jorge Frias-Lopez
Imbalances of the microbiome, also referred to as microbial dysbiosis, could lead to a series of different diseases. One factor that has been shown to lead to dysbiosis of the microbiome is exposure to psychological stressors. Throughout evolution microorganisms of the human microbiome have developed systems for sensing host-associated signals such as hormones associated with those stressors, enabling them to recognize essential changes in their environment, thus changing their expression gene profile to fit the needs of the new environment...
2018: NPJ Biofilms and Microbiomes
Julia Y Co, Gerardo Cárcamo-Oyarce, Nicole Billings, Kelsey M Wheeler, Scott C Grindy, Niels Holten-Andersen, Katharina Ribbeck
Mucus is a biological gel that lines all wet epithelia in the body, including the mouth, lungs, and digestive tract, and has evolved to protect the body from pathogenic infection. However, microbial pathogenesis is often studied in mucus-free environments that lack the geometric constraints and microbial interactions in physiological three-dimensional mucus gels. We developed fluid-flow and static test systems based on purified mucin polymers, the major gel-forming constituents of the mucus barrier, to understand how the mucus barrier influences bacterial virulence, particularly the integrity of Pseudomonas aeruginosa biofilms, which can become resistant to immune clearance and antimicrobial agents...
2018: NPJ Biofilms and Microbiomes
Thammajun L Wood, Ting Gong, Lei Zhu, James Miller, Daniel S Miller, Bei Yin, Thomas K Wood
Biofilm formation is an important problem for many industries. Desulfovibrio vulgaris is the representative sulfate-reducing bacterium (SRB) which causes metal corrosion in oil wells and drilling equipment, and the corrosion is related to its biofilm formation. Biofilms are extremely difficult to remove since the cells are cemented in a polymer matrix. In an effort to eliminate SRB biofilms, we examined the ability of supernatants from Pseudomonas aeruginosa PA14 to disperse SRB biofilms. We found that the P ...
2018: 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
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