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NPJ Biofilms and Microbiomes

Ezequiel Santillan, Hari Seshan, Florentin Constancias, Daniela I Drautz-Moses, Stefan Wuertz
Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days...
2019: NPJ Biofilms and Microbiomes
Danielle M Vermilyea, Gregory K Ottenberg, Mary E Davey
Porphyromonas gingivalis is the only known human-associated prokaryote that produces a peptidylarginine deiminase (PPAD), a protein-modifying enzyme that is secreted along with a number of virulence factors via a type IX secretion system (T9SS). While the function of PPAD in P. gingivalis physiology is not clear, human peptidylarginine deiminases are known to convert positively charged arginine residues within proteins to neutral citrulline and, thereby, impact protein conformation and function. Here, we report that the lack of citrullination in a PPAD deletion mutant (Δ8820) enhances biofilm formation...
2019: NPJ Biofilms and Microbiomes
Hendrik J de Vries, Florian Beyer, Monika Jarzembowska, Joanna Lipińska, Paula van den Brink, Arie Zwijnenburg, Peer H A Timmers, Alfons J M Stams, Caroline M Plugge
Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes...
2019: NPJ Biofilms and Microbiomes
Marie Lindefeldt, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, Stefanie Prast-Nielsen
The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes...
2019: NPJ Biofilms and Microbiomes
Mehdi Layeghifard, Hannah Li, Pauline W Wang, Sylva L Donaldson, Bryan Coburn, Shawn T Clark, Julio Diaz Caballero, Yu Zhang, D Elizabeth Tullis, Yvonne C W Yau, Valerie Waters, David M Hwang, David S Guttman
Over 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading to respiratory failure. The decline in CF lung function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach to identify key members of the microbiota. We used two CF sputum microbiome data sets that were longitudinally collected through periods spanning baseline health and PEs...
2019: NPJ Biofilms and Microbiomes
Ashutosh Kumar, Anwar Alam, Sonam Grover, Saurabh Pandey, Deeksha Tripathi, Monika Kumari, Mamta Rani, Aditi Singh, Yusuf Akhter, Nasreen Z Ehtesham, Seyed E Hasnain
Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis ( M.tb ), takes one human life every 15 s globally. Disease relapse occurs due to incomplete clearance of the pathogen and reactivation of the antibiotic tolerant bacilli. M.tb , like other bacterial pathogens, creates an ecosystem of biofilm formed by several proteins including the cyclophilins. We show that the M.tb cyclophilin peptidyl-prolyl isomerase (PpiB), an essential gene, is involved in biofilm formation and tolerance to anti-mycobacterial drugs...
2019: NPJ Biofilms and Microbiomes
Yingying Cheng, Joey Kuok Hoong Yam, Zhao Cai, Yichen Ding, Lian-Hui Zhang, Yinyue Deng, Liang Yang
Pseudomonas aeruginosa tends to be among the dominant species in multi-species bacterial consortia in diverse environments. To understand P. aeruginosa's physiology and interactions with co-existing bacterial species in different conditions, we established physiologically reproducible 18 species communities, and found that P. aeruginosa dominated in mixed-species biofilm communities but not in planktonic communities. P. aeruginosa's H1 type VI secretion system was highly induced in mixed-species biofilm consortia, compared with its monospecies biofilm, which was further demonstrated to play a key role in P...
2019: NPJ Biofilms and Microbiomes
Julia L Drewes, James R White, Christine M Dejea, Payam Fathi, Thevambiga Iyadorai, Jamuna Vadivelu, April C Roslani, Elizabeth C Wick, Emmanuel F Mongodin, Mun Fai Loke, Kumar Thulasi, Han Ming Gan, Khean Lee Goh, Hoong Yin Chong, Sandip Kumar, Jane W Wanyiri, Cynthia L Sears
[This corrects the article DOI: 10.1038/s41522-017-0040-3.].
2019: NPJ Biofilms and Microbiomes
Mária Džunková, Daniel Martinez-Martinez, Roman Gardlík, Michal Behuliak, Katarína Janšáková, Nuria Jiménez, Jorge F Vázquez-Castellanos, Jose Manuel Martí, Giuseppe D'Auria, H M H N Bandara, Amparo Latorre, Peter Celec, Andrés Moya
The term "bacterial dysbiosis" is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21...
2018: NPJ Biofilms and Microbiomes
Angela Zou, Shayan Sharif, John Parkinson
The poultry industry has traditionally relied on the use of antibiotic growth promoters (AGPs) to improve production efficiency and minimize infection. With the recent drive to eliminate the use of AGPs, novel alternatives are urgently required. Recently attention has turned to the use of synthetic communities that may be used to 'seed' the developing microbiome. The current challenge is identifying keystone taxa whose influences in the gut can be leveraged for probiotic development. To help define such taxa we present a meta-analysis of 16S rRNA surveys of 1572 cecal microbiomes generated from 19 studies...
2018: 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
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