Patterns of the fecal microbiota in the Juan Fern ández fur seal (Arctocephalus philippii)
This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host –microbial–environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 r egion of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla:Firmicutes (40% ±24),Fusobacteria (30% ±17),Bacteroidetes (22% ±10),Proteobacteria (6% ±4), andAc...
Source: MicrobiologyOpen - July 23, 2021 Category: Microbiology Authors: Constanza Toro ‐Valdivieso,
Frederick Toro,
Samuel Stubbs,
Eduardo Castro‐Nallar,
Barbara Blacklaws Tags: ORIGINAL ARTICLE Source Type: research
Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile
We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. The 16S rRNA gene of a hyperthermophile,Thermus aquaticus, was cloned intoPichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before high-throughput sequencing and 16S rRNA gene amplicon analysis. The absolute abundances of bacteria were calculated usingT. aquaticus reads. AbstractHigh-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of...
Source: MicrobiologyOpen - July 23, 2021 Category: Microbiology Authors: Ju Yeong Kim,
Myung ‐hee Yi,
Myungjun Kim,
Seogwon Lee,
Hye Su Moon,
Dongeun Yong,
Tai‐Soon Yong Tags: ORIGINAL ARTICLE Source Type: research
Schiff bases of sulphonamides as a new class of antifungal agent against multidrug ‐resistant Candida auris
We report a new class of antifungal agents, the Schiff bases of sulphonamides, that show activity against allCandida species tested including multidrug-resistantC. auris. The drug-like nature of these Schiff bases offers opportunities to optimize these compounds with medicinal chemistry techniques to obtain more potent analogs that can be progressed toward pre-clinical evaluation. AbstractInvasiveCandida infections in hospitalized and immunocompromised or critically ill patients have become an important cause of morbidity and mortality. There are increasing reports of multidrug resistance in severalCandida species that c...
Source: MicrobiologyOpen - July 23, 2021 Category: Microbiology Authors: Asad Hamad,
Yiyuan Chen,
Mohsin A. Khan,
Shirin Jamshidi,
Naima Saeed,
Melanie Clifford,
Charlotte Hind,
J. Mark Sutton,
Khondaker Miraz Rahman Tags: ORIGINAL ARTICLE Source Type: research
Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf ‐5
Oil sands mining operations produce vast amounts of oil sands process-affected waters (OSPW) that contain recalcitrant and toxic naphthenic acids (NAs), yet little is known about the mechanisms of NA biodegradation and the enzymes involved. Here, we identified several proteins overexpressed inPseudomonas fluorescens Pf-5 during growth on NAs and included multiple transporters (e.g. ABC transporters), suggesting a cellular protective response from NA toxicity, alongside proteins associated with the fatty acid, lipid, and amino acid metabolism. We postulate thatP. fluorescens Pf-5 is using existing fatty acid catabolic pathw...
Source: MicrobiologyOpen - July 21, 2021 Category: Microbiology Authors: Boyd A. McKew,
Richard Johnson,
Lindsay Clothier,
Karl Skeels,
Matthew S. Ross,
Metodi Metodiev,
Max Frenzel,
Lisa M. Gieg,
Jonathan W. Martin,
Michael A. Hough,
Corinne Whitby Tags: ORIGINAL ARTICLE Source Type: research
The c ‐di‐AMP signaling system influences stress tolerance and biofilm formation of Streptococcus mitis
In this study, we utilizedS. mitis deletion mutants ofcdaA,pde1, andpde2 to analyze the role of c-di-AMP signaling in various stress responses, biofilm formation, and adhesion to eukaryotic cells. Here, we demonstrate that the Δpde1 mutant displayed a tendency toward increased susceptibility to acetic acid at pH 4.0. Deletion ofcdaA increases auto-aggregation ofS. mitis but reduces biofilm formation on an abiotic surface. These phenotypes are more pronounced under acidic extracellular conditions. Inactivation ofpde1 orpde2 reduced the tolerance to ciprofloxacin, and UV radiation and the Δpde1 mutant was more suscepti...
Source: MicrobiologyOpen - July 19, 2021 Category: Microbiology Authors: Gro Herredsvela R ørvik,
Ali‐Oddin Naemi,
Per Kristian Thorén Edvardsen,
Roger Simm Tags: ORIGINAL ARTICLE Source Type: research
Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution ‐derived hydrogen
This study provides a detailed characterization of the geochemistry and bacterial community inhabiting the subglacial basal ice layer of three Icelandic glaciers. Our data show that a thriving chemolithotroph-powered community exists within basal ice, fuelled by the oxidation of hydrogen and iron. AbstractThe basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly d...
Source: MicrobiologyOpen - July 19, 2021 Category: Microbiology Authors: Mario Toubes ‐Rodrigo,
Sanja Potgieter‐Vermaak,
Robin Sen,
Edda S. Oddsdóttir,
David Elliott,
Simon Cook Tags: ORIGINAL ARTICLE Source Type: research
The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae)
We have previously shown that the fungal and bacterial communities in nests of antsFormicaexsecta are distinct from those in the surrounding soil. Now, the results from our three-year study show that the nests also provide a temporally stable environment, where microbial taxa, less tolerant of climatic fluctuations, could survive through unfavorable seasons. The nest could thus act as a reservoir for such microbial inocula, promoting the divergence of the nest communities over time. AbstractIn a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial...
Source: MicrobiologyOpen - July 19, 2021 Category: Microbiology Authors: Stafva Lindstr öm,
Sari Timonen,
Liselotte Sundström Tags: ORIGINAL ARTICLE Source Type: research
Issue Information
(Source: MicrobiologyOpen)
Source: MicrobiologyOpen - July 16, 2021 Category: Microbiology Tags: ISSUE INFORMATION Source Type: research
Machine learning modeling of the effects of media formulated with various yeast extracts on heterologous protein production in Escherichia coli
A deep neural network-mediated optimization of bacterial medium for producing green fluorescence protein as a model of heterogeneous protein by an engineeredEscherichia coli is demonstrated in this article. Using gas chromatography/mass spectrometry profiling for the medium components including various yeast extracts, a deep learning algorithm estimated the culture from the profiling with preferable accuracy, and permutation algorithm and sensitivity analysis with the trained model estimated significant components. Supplementation of the components led to improve growth and protein production. AbstractIn microbial manufact...
Source: MicrobiologyOpen - June 28, 2021 Category: Microbiology Authors: Seiga Tachibana,
Tai ‐Ying Chiou,
Masaaki Konishi Tags: ORIGINAL ARTICLE Source Type: research
Deletion of Rap ‐Phr systems in Bacillus subtilis influences in vitro biofilm formation and plant root colonization
Bacillussubtilis NCIB3610 contains 12 cell –cell signaling Rap-Phr systems that influence cell differentiation. Here, we systematically investigate how each of these systems impacts biofilm formation by studying WT and the 12 single ∆rap-phr mutants in different phenotypic assays. Our approach revealed that while all 12 Rap-Phr systems affect matrix gene expression, only certain Rap-Phr systems influence the development ofin vitro biofilms and root colonization, the latter representing an ecologically relevant environment for this bacterium. AbstractNatural isolates of the soil-dwelling bacteriumBacillussubtilis form r...
Source: MicrobiologyOpen - June 27, 2021 Category: Microbiology Authors: Mathilde Nordgaard,
Rasmus M øller Rosenbek Mortensen,
Nikolaj Kaae Kirk,
Ramses Gallegos‐Monterrosa,
Ákos T. Kovács Tags: ORIGINAL ARTICLE Source Type: research
Cultivation of the gut bacterium Prevotella copri DSM 18205T using glucose and xylose as carbon sources
This study presents successful batch cultivation strategies for viable strain inoculations and growth in both serum bottles and a stirred tank bioreactor (STR), without the use of an anaerobic chamber, as long as the cells were kept in the exponential growth phase. A low headspace volume in the STR was important to reach high cell density.P.copri utilized xylose cultivated in Peptone Yeast Xylose medium (PYX medium), resulting in a comparable growth rate and metabolite production as in Peptone Yeast Glucose medium (PYG medium) in batch cultivations at pH 7.2.Up to 5 g/L of the carbon source was consumed, leading to the p...
Source: MicrobiologyOpen - June 27, 2021 Category: Microbiology Authors: Fang Huang,
Roya R. R. Sardari,
Andrius Jasilionis,
Olof B öök,
Rickard Öste,
Ana Rascón,
Lovisa Heyman‐Lindén,
Olle Holst,
Eva Nordberg Karlsson Tags: ORIGINAL ARTICLE Source Type: research
Niche partitioning of bacterial communities along the stratified water column in the Black Sea
The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. It is suggested that regional differentiation within a well-oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the bacteria, whereas redox stratification is the main driving force behind microbial community vertical structure. AbstractThe Black Sea is the largest semi-closed permanently anoxic basin on our planet with long...
Source: MicrobiologyOpen - June 22, 2021 Category: Microbiology Authors: Mariia Pavlovska,
Ievgeniia Prekrasna,
Evgen Dykyi,
Andrii Zotov,
Artem Dzhulai,
Alina Frolova,
Jaroslav Slobodnik,
Elena Stoica Tags: ORIGINAL ARTICLE Source Type: research
Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis
By demonstrating that clear transmission relationships exist among groups ofMycobacterium tuberculosis clinical isolates via whole genome sequence comparisons and SNP threshold analysis, the corresponding epidemiological data can be used to confirm these linkages and ultimately provide an improved mechanism to design and implement control strategies within geographic regions such as Kampala, Uganda. AbstractTuberculosis (TB) is the leading cause of death in humans by a single infectious agent worldwide with approximately two billion humans latently infected with the bacteriumMycobacterium tuberculosis. Currently, the accep...
Source: MicrobiologyOpen - June 17, 2021 Category: Microbiology Authors: Edriss Yassine,
Ronald Galiwango,
Willy Ssengooba,
Fred Ashaba,
Moses L. Joloba,
Sarah Zalwango,
Christopher C. Whalen,
Frederick Quinn Tags: ORIGINAL ARTICLE Source Type: research
Direct detection of ESKAPEc pathogens from whole blood using the T2Bacteria Panel allows early antimicrobial stewardship intervention in patients with sepsis
The T2Bacteria Panel allows for fast and reliable detection of the six most common bloodstream infection pathogens. Its sensitivity of on-panel pathogens was 94% compared with blood cultures (53%). It detected pathogens on average 55 hours faster than using standard blood cultures. Given the high reliability, faster time to detection and easy workflow, the technique qualifies as a point-of-care testing approach. AbstractIn the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FD...
Source: MicrobiologyOpen - June 17, 2021 Category: Microbiology Authors: Pavel Drevinek,
Jakub Hurych,
Milena Antuskova,
Jan Tkadlec,
Jan Berousek,
Zuzana Prikrylova,
Jiri Bures,
Jaromir Vajter,
Martin Soucek,
Jan Masopust,
Vendula Martinkova,
Jaroslava Adamkova,
Veronika Hysperska,
Eliska Bebrova Tags: ORIGINAL ARTICLE Source Type: research
Optimized bacterial DNA isolation method for microbiome analysis of human tissues
We present a bacterial DNA isolation method for human colon biopsies which includes reduction of human DNA and does not distort relative bacterial abundance at the phylum level. Shotgun sequencing resulted in 508/521 metagenomes (Shannon index; 2.9, UniFrac distance; 0.56). Fifteen colon biopsies were sequenced by both amplicon and shotgun sequencing resulting in similar bacterial profiles from phylum to genus level. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research. AbstractRecent advances in microbiome sequencing have rendered...
Source: MicrobiologyOpen - June 16, 2021 Category: Microbiology Authors: Carlijn E. Bruggeling,
Daniel R. Garza,
Soumia Achouiti,
Wouter Mes,
Bas E. Dutilh,
Annemarie Boleij Tags: ORIGINAL ARTICLE Source Type: research
