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NPJ Biofilms and Microbiomes

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https://www.readbyqxmd.com/read/29707230/a-tad-pilus-promotes-the-establishment-and-resistance-of-vibrio-vulnificus-biofilms-to-mechanical-clearance
#1
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
https://www.readbyqxmd.com/read/29707229/fighting-biofilms-with-lantibiotics-and-other-groups-of-bacteriocins
#2
REVIEW
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
https://www.readbyqxmd.com/read/29675263/micro-ct-x-ray-imaging-exposes-structured-diffusion-barriers-within-biofilms
#3
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
https://www.readbyqxmd.com/read/29619241/ugly-ducklings-the-dark-side-of-plastic-materials-in-contact-with-potable-water
#4
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
https://www.readbyqxmd.com/read/29560270/how-do-environment-dependent-switching-rates-between-susceptible-and-persister-cells-affect-the-dynamics-of-biofilms-faced-with-antibiotics
#5
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
https://www.readbyqxmd.com/read/29531777/net-growth-rate-of-continuum-heterogeneous-biofilms-with-inhibition-kinetics
#6
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
https://www.readbyqxmd.com/read/29507749/precision-antimicrobial-therapeutics-the-path-of-least-resistance
#7
REVIEW
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
https://www.readbyqxmd.com/read/29479470/tools-for-studying-growth-patterns-and-chemical-dynamics-of-aggregated-pseudomonas-aeruginosa-exposed-to-different-electron-acceptors-in-an-alginate-bead-model
#8
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
https://www.readbyqxmd.com/read/29367879/advantages-of-meta-total-rna-sequencing-metrs-over-shotgun-metagenomics-and-amplicon-based-sequencing-in-the-profiling-of-complex-microbial-communities
#9
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
https://www.readbyqxmd.com/read/29367878/coastal-urbanisation-affects-microbial-communities-on-a-dominant-marine-holobiont
#10
Ezequiel M Marzinelli, Zhiguang Qiu, Katherine A Dafforn, Emma L Johnston, Peter D Steinberg, Mariana Mayer-Pinto
Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity...
2018: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29214047/high-resolution-profiling-of-the-gut-microbiome-reveals-the-extent-of-clostridium-difficile-burden
#11
Ninalynn Daquigan, Anna Maria Seekatz, K Leigh Greathouse, Vincent B Young, James Robert White
Microbiome profiling through 16S rRNA gene sequence analysis has proven to be a useful research tool in the study of C. difficile infection (CDI); however, CDI microbiome studies typically report results at the genus level or higher, thus precluding identification of this pathogen relative to other members of the gut microbiota. Accurate identification of C. difficile relative to the overall gut microbiome may be useful in assessments of colonization in research studies or as a prognostic indicator for patients with CDI...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29214046/high-resolution-bacterial-16s-rrna-gene-profile-meta-analysis-and-biofilm-status-reveal-common-colorectal-cancer-consortia
#12
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
Colorectal cancer (CRC) remains the third most common cancer worldwide, with a growing incidence among young adults. Multiple studies have presented associations between the gut microbiome and CRC, suggesting a link with cancer risk. Although CRC microbiome studies continue to profile larger patient cohorts with increasingly economical and rapid DNA sequencing platforms, few common associations with CRC have been identified, in part due to limitations in taxonomic resolution and differences in analysis methodologies...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29214045/the-rumen-microbiome-an-underexplored-resource-for-novel-antimicrobial-discovery
#13
Linda B Oyama, Susan E Girdwood, Alan R Cookson, Narcis Fernandez-Fuentes, Florence Privé, Hannah E Vallin, Toby J Wilkinson, Peter N Golyshin, Olga V Golyshina, Ralf Mikut, Kai Hilpert, Jennifer Richards, Mandy Wootton, Joan E Edwards, Marc Maresca, Josette Perrier, Fionnuala T Lundy, Yu Luo, Mei Zhou, Matthias Hess, Hilario C Mantovani, Christopher J Creevey, Sharon A Huws
Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA)...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29177068/carbonate-rich-dendrolitic-cones-insights-into-a-modern-analog-for-incipient-microbialite-formation-little-hot-creek-long-valley-caldera-california
#14
James A Bradley, Leslie K Daille, Christopher B Trivedi, Caitlin L Bojanowski, Blake W Stamps, Bradley S Stevenson, Heather S Nunn, Hope A Johnson, Sean J Loyd, William M Berelson, Frank A Corsetti, John R Spear
Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool ("Cone Pool") at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29152323/new-melanocortin-like-peptide-of-e-coli-can-suppress-inflammation-via-the-mammalian-melanocortin-1-receptor-mc1r-possible-endocrine-like-function-for-microbes-of-the-gut
#15
Xiaoling Qiang, Anthony S Liotta, Joseph Shiloach, J C Gutierrez, Haichao Wang, Mahendar Ochani, Kanta Ochani, Huan Yang, Aviva Rabin, Derek LeRoith, Maxine A Lesniak, Markus Böhm, Christian Maaser, Klaus Kannengiesser, Mark Donowitz, Shervin Rabizadeh, Christopher J Czura, Kevin J Tracey, Mark Westlake, Aida Zarfeshani, Syed F Mehdi, Ann Danoff, Xueliang Ge, Suparna Sanyal, Gary J Schwartz, Jesse Roth
E. coli releases a 33 amino acid peptide melanocortin-like peptide of E. coli (MECO-1) that is identical to the C-terminus of the E. coli elongation factor-G (EF-G) and has interesting similarities to two prominent mammalian melanocortin hormones, alpha-melanocyte-stimulating hormone (alpha-MSH) and adrenocorticotropin (ACTH). Note that MECO-1 lacks HFRW, the common pharmacophore of the known mammalian melanocortin peptides. MECO-1 and the two hormones were equally effective in severely blunting release of cytokines (HMGB1 and TNF) from macrophage-like cells in response to (i) endotoxin (lipopolysaccharide) or (ii) pro-inflammatory cytokine HMGB-1...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29134109/erratum-author-correction-norgestimate-inhibits-staphylococcal-biofilm-formation-and-resensitizes-methicillin-resistant-staphylococcus-aureus-to-%C3%AE-lactam-antibiotics
#16
Yutaka Yoshii, Ken-Ichi Okuda, Satomi Yamada, Mari Nagakura, Shinya Sugimoto, Tetsuo Nagano, Takayoshi Okabe, Hirotatsu Kojima, Takeo Iwamoto, Kazuyoshi Kuwano, Yoshimitsu Mizunoe
[This corrects the article DOI: 10.1038/s41522-017-0026-1.].
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29134108/host-and-bacterial-proteases-influence-biofilm-formation-and-virulence-in-a-murine-model-of-enterococcal-catheter-associated-urinary-tract-infection
#17
Wei Xu, Ana L Flores-Mireles, Zachary T Cusumano, Enzo Takagi, Scott J Hultgren, Michael G Caparon
Enterococcus faecalis is a leading causative agent of catheter-associated urinary tract infection (CAUTI), the most common hospital-acquired infection. Its ability to grow and form catheter biofilm is dependent upon host fibrinogen (Fg). Examined here are how bacterial and host proteases interact with Fg and contribute to virulence. Analysis of mutants affecting the two major secreted proteases of E. faecalis OG1RF (GelE, SprE) revealed that while the loss of either had no effect on virulence in a murine CAUTI model or for formation of Fg-dependent biofilm in urine, the loss of both resulted in CAUTI attenuation and defective biofilm formation...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29114399/erratum-author-correction-identification-of-donor-microbe-species-that-colonize-and-persist-long-term-in-the-recipient-after-fecal-transplant-for-recurrent-clostridium-difficile
#18
Ranjit Kumar, Nengjun Yi, Degui Zhi, Peter Eipers, Kelly T Goldsmith, Paula Dixon, David K Crossman, Michael R Crowley, Elliot J Lefkowitz, J Martin Rodriguez, Casey D Morrow
[This corrects the article DOI: 10.1038/s41522-017-0020-7.].
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29104759/human-microbiome-signatures-of-differential-colorectal-cancer-drug-metabolism
#19
Leah Guthrie, Sanchit Gupta, Johanna Daily, Libusha Kelly
It is well appreciated that microbial metabolism of drugs can influence treatment efficacy. Microbial β-glucuronidases in the gut can reactivate the excreted, inactive metabolite of irinotecan, a first-line chemotherapeutic for metastatic colorectal cancer. Reactivation causes adverse drug responses, including severe diarrhea. However, a direct connection between irinotecan metabolism and the composition of an individual's gut microbiota has not previously been made. Here, we report quantitative evidence of inter-individual variability in microbiome metabolism of the inactive metabolite of irinotecan to its active form...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29081982/the-making-of-a-miscreant-tobacco-smoke-and-the-creation-of-pathogen-rich-biofilms
#20
Samir A Shah, Sukirth M Ganesan, Saradhadevi Varadharaj, Shareef M Dabdoub, John D Walters, Purnima S Kumar
We have previously reported that oral biofilms in clinically healthy smokers are pathogen-rich, and that this enrichment occurs within 24 h of biofilm formation. The present investigation aimed to identify a mechanism by which smoking creates this altered community structure. By combining in vitro microbial-mucosal interface models of commensal (consisting of Streptococcus oralis, Streptococcus sanguis, Streptococcus mitis, Actinomyces naeslundii, Neisseria mucosa and Veillonella parvula) and pathogen-rich (comprising S...
2017: NPJ Biofilms and Microbiomes
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