Integrative Genome Assembly of Staphylococcus epidermidis and Staphylococcus hominis Strains

Due to rapid advances in sequencing technology, it is becoming increasingly easier to assemble unknown genomes from millions of short sequencing reads of nucleotides taken from the full genomic sequence (Hernandez, 2008). In this study, we used various computational programs to align reads from unsequenced strains of the bacteria Staphylococcus epidermidis and Staphylococcus hominis into a hitherto undefined, single contiguous genomic sequence. We used SPAdes to assist with template free assembly (Bankevich, 2012), BLAST to identify a suitable reference genome from closely related species (Madden, 2013), Bowtie2 to align our reads to the reference genome, SAMtools to sort and organize files (Li, 2009), RGAAT to incorporate variants into our reads and update our final genome (Liu, 2018), and Mauve to rapidly align the reads and provide a visual representation of the final genome (Darling, 2011). In all, we assembled ten bacterial genomes which have never been sequenced and assembled previously. Importantly, we have developed and validated a high throughput computational pipeline capable of quickly assembling full genomes from millions of individual reads. Excitingly this protocol can continue to be used as needed to sequence and assemble more bacterial genomes to provide a genetic basis for studying bacterial characteristics

Next-Generation Probiotics Targeting \u3ci\u3eClostridium difficile\u3c/i\u3e through Precursor- Directed Antimicrobial Biosynthesis

Integration of antibiotic and probiotic therapy has the potential to lessen the public health burden of antimicrobial-associated diseases. Clostridium difficile infection (CDI) represents an important example where the rational design of next-generation probiotics is being actively pursued to prevent disease recurrence. Because intrinsic resistance to clinically relevant antibiotics used to treat CDI (vancomycin, metronidazole, and fidaxomicin) is a desired trait in such probiotic species, we screened several bacteria and identified Lactobacillus reuteri to be a promising candidate for adjunct therapy. Human-derived L. reuteri bacteria convert glycerol to the broad-spectrum antimicrobial compound reuterin. When supplemented with glycerol, strains carrying the pocR gene locus were potent reuterin producers, with L. reuteri 17938 inhibiting C. difficile growth at a level on par with the level of growth inhibition by vancomycin. Targeted pocR mutations and complementation studies identified reuterin to be the precursor-induced antimicrobial agent. Pathophysiological relevance was demonstrated when the codelivery of L. reuteri with glycerol was effective against C. difficile colonization in complex human fecal microbial communities, whereas treatment with either glycerol or L. reuteri alone was ineffective. A global unbiased microbiome and metabolomics analysis independently confirmed that glycerol precursor delivery with L. reuteri elicited changes in the composition and function of the human microbial community that preferentially targets C. difficile outgrowth and toxicity, a finding consistent with glycerol fermentation and reuterin production. Antimicrobial resistance has thus been successfully exploited in the natural design of human microbiome evasion of C. difficile, and this method may provide a prototypic precursor-directed probiotic approach. Antibiotic resistance and substrate bioavailability may therefore represent critical new determinants of probiotic efficacy in clinical trials

The South Atlantic circulation between 34.5°S, 24°S and above the Mid‐Atlantic Ridge from an inverse box model

The South Atlantic Ocean plays a key role in the heat exchange of the climate system, as it hosts the returning flow of the Atlantic Meridional Overturning Circulation (AMOC). To gain insights on this role, using data from three hydrographic cruises conducted in the South Atlantic Subtropical gyre at 34.5°S, 24°S, and 10°W, we identify water masses and compute absolute geostrophic circulation using inverse modeling. In the upper layers, the currents describe the South Atlantic anticyclonic gyre with the northwest flowing Benguela Current (26.3 ± 2.0 Sv at 34.5°S, and 21.2 ± 1.8 Sv at 24°S) flowing above the Mid-Atlantic Ridge (MAR) between 22.4°S and 28.4°S (−19.2 ± 1.4 Sv), and the southward flowing Brazil Current (−16.5 ± 1.3 Sv at 34.5°S, and −7.3 ± 0.9 Sv at 24°S); the deep layers feature the southward transports of Deep Western Boundary Current (−13.9 ± 3.0 Sv at 34.5°S, and −8.7 ± 3.8 Sv at 24°S) and Deep Eastern Boundary Current (−15.1 ± 3.5 Sv at 34.5°S, and −16.3 ± 4.7 Sv at 24°S), with the interbasin west-to-east flow close to 24°S (7.5 ± 4.4 Sv); the abyssal waters present northward mass transports through the Argentina Basin (5.6 ± 1.1 Sv at 34.5°S, and 5.8 ± 1.5 Sv at 24°S) and Cape Basin (8.6 ± 3.5 Sv at 34.5°S–3.0 ± 0.8 Sv at 24°S) before returning southward (−2.2 ± 0.7 Sv at 24°S to −7.9 ± 3.6 Sv at 34.5°S), without any interbasin exchange across the MAR. In addition, we compute the upper AMOC strength (14.8 ± 1.0 and 17.5 ± 0.9 Sv), the equatorward heat transport (0.30 ± 0.05 and 0.80 ± 0.05 PW), and the freshwater flux (0.18 ± 0.02 and −0.07 ± 0.02 Sv) at 34.5°S and 24°S, respectively

Analysis of the atmosphere behaviour in the proximities of an orographic obstacle

The atmospheric behaviour near an orographic obstacle has been thoroughly studied in the last decades. The first papers in this field were mainly theoretical, being more recent the laboratory experiments which represented that behaviour in ideal conditions. The numerical simulations have been addressed lately thanks to the development of computers. But the study of meteorology in complex terrain has lacked experiments in the atmosphere to understand the real influence the relief has on it. <br> In this paper the problem has been considered from the last perspective, and so, seasons of measure of the atmospheric variables within the boundary layer have been organized with the goal of checking existing theories and bringing right conclusions from real experiment in the atmosphere. <br> Controverted aspects of linear and nonlinear theories, as the location of critical points upwind and downwind of an orographic obstacle, will be analyzed. The results obtained show a large adequacy between the forecasted behaviour and the experimentally detected

Mesoscale convective complexes over the western Mediterranean area during 1990-1994

Mesoscale Convective Systems (MCSs) data registers from June to December during 1990-94 were obtained from the Spanish National Meteorological Institute (INM). Fifteen Mesoscale Convective Complexes (MCCs) were identified through this database. Most of the MCCs developed during the last week of September. The dominant synoptic patterns related to the mesoscale systems were cold fronts at the surface with warm and moist low-level cores, and cut-off low or deep trough throughout the middle and upper levels. These synoptic patterns were found in all the fifteen cases studied. The hourly centroid location of each MCC was used to trace their tracks, which followed a general direction towards the E or NE in almost all cases. These trajectories are clearly related to the synoptic patterns found. Finally, two MCCs chosen as representative of their evolution are described and the related physical processes are discussed

plcR papR-Independent Expression of Anthrolysin O by Bacillus anthracis

Cholesterol-dependent cytolysins (CDCs) are secreted, pore-forming toxins that are associated with pathogenesis in a variety of gram-positive bacteria. Bacillus anthracis produces anthrolysin O (ALO), a CDC that is largely responsible for the hemolytic activity of culture supernates when the bacterium is cultured in appropriate conditions. B. cereus and B. thuringiensis, species closely related to B. anthracis, produce CDCs with significant amino acid sequence homology to ALO. Transcription of the B. cereus and B. thuringiensis CDC genes is controlled by PlcR, a transcription regulator that requires a pentapeptide derived from the papR gene product for binding to a consensus sequence (PlcR box) and transcriptional activation of downstream genes. A PlcR box precedes the B. anthracis alo gene, and the B. anthracis genome contains three plcR-like genes, one of which harbors a nonsense mutation that is predicted to result in a truncated, nonfunctional protein. We detected mRNA of alo, papR, and the three plcR-like genes in spleens of B. anthracis-infected mice, indicating gene expression in vivo. Analysis of alo transcription in batch culture revealed a potential transcription start located between the PlcR box and the translational start. Nevertheless, steady-state levels of alo transcripts and ALO protein were unaffected by deletion of papR or disruption of the PlcR box. Our data indicate that despite the presence of the transcriptionally active plcR and papR genes in B. anthracis and a PlcR box in the promoter region of the alo gene, alo expression is independent of this control system

An Extracytoplasmic Function Sigma Factor Controls β-Lactamase Gene Expression in Bacillus anthracis and Other Bacillus cereus Group Species▿ †

The susceptibility of most Bacillus anthracis strains to β-lactam antibiotics is intriguing considering that the closely related species Bacillus cereus and Bacillus thuringiensis typically produce β-lactamases and the B. anthracis genome harbors two β-lactamase genes, bla1 and bla2. We show that β-lactamase activity associated with B. anthracis is affected by two genes, sigP (BA2502) and rsiP (BA2503), predicted to encode an extracytoplasmic function sigma factor and an anti-sigma factor, respectively. Deletion of the sigP-rsiP locus abolished β-lactamase activity in a naturally occurring penicillin-resistant strain and had no effect on β-lactamase activity in a prototypical penicillin-susceptible strain. Complementation with sigP and rsiP from the penicillin-resistant strain, but not with sigP and rsiP from the penicillin-susceptible strain, conferred constitutive β-lactamase activity in both mutants. These results are attributed to a nucleotide deletion near the 5′ end of rsiP in the penicillin-resistant strain that is predicted to result in a nonfunctional protein. B. cereus and B. thuringiensis sigP and rsiP homologues are required for inducible penicillin resistance in these species. Expression of the B. cereus or B. thuringiensis sigP and rsiP genes in a B. anthracis sigP-rsiP-null mutant confers inducible production of β-lactamase activity, suggesting that while B. anthracis contains the genes necessary for sensing β-lactam antibiotics, the B. anthracis sigP and rsiP gene products are not sufficient for bla induction