Search

I copri i was previously reported to be significantly decreased but still present in the gut of children with AD compared to healthy controls in ASA.7 This species was further depleted and nearly absent in the majority of AA children with AD. Microbiome of the skin and gut in atopic dermatitis (AD): understanding the pathophysiology and finding novel management strategies. Keywords: atopic dermatitis; epidemiology; food allergy; omics- and systems biology; pediatrics EN atopic dermatitis epidemiology food allergy omics- and systems biology pediatrics 447 450 4 02/24/22 20220301 NES 220301 Key Messages African-heritage children with eczema from Chicago have lower microbiota diversity compared to children from South Africa. Atopic dermatitis, epidemiology, food allergy, omics- and systems biology, pediatrics. [Extracted from the article]

A study was conducted to test whether the RecA protein of Escherichia coli, UTP, can substitute for adenosine triphosphate (ATP) in DNA strand exchange reactions influenced by RecA protein in vitro. A thin-layer chromatography assay was utilized to observe the hydrolysis of nucleotide triphosphates while wild-type RecA protein was determined from E. coli strain GE1171. Results showed that UTP can substitute for ATP in DNA strand exchange reactions.

Treponema pallidum is different from other spirochetes because it contains cytoplasmic filaments underneath the cytoplasmic membrane. Cloning and expression of the cytoplasmic filament protein gene cfpA of Treponema pallidum subsp. pallidum Nichols identified three components of the gene: a 2,034-nucleotide coding region; a putative promoter region; and a putative ribosome-binding site. Sequence analysis indicated a protein of 678 residues with a molecular mass of 78.5 kilodaltons and an isoelectric potential of 6.15. It was suggested that T. pallidum cytoplasmic filaments may be a unique form of prokaryotic intracytoplasmic inclusions.

Increase in the expression of cea-lacZ fusions and production of colicin E1 in bacteria during the stationary phase of the cells are caused by the lack of nutrients from the medium. Expression of the fusion increased when cells were starved in 10 mM MgSO4 and when they were grown in conditioned medium in which cells have been grown previously. The increase is not due to SOS response, anaerobiosis, catabolite repression, integration host factor and the stationary-phase regulators encoded by rpoS and lrp.

A novel method is used to compare the pairwise structures of RecA protein sequences from 62 eubacterial sources. Results show that the eubacterial sources can be classified into two major groups, those of mostly vertebrate hosts and those of mostly soil habitat. The data also suggests that the bacteriophage T4 UvX protein aligns best with RecA sequences on two segments disjoint from the ATP-binding domain.

The feasibility of using allelic replacement to generate enterococcal pyr and pur auxotrophs of Enterococcus faecalis is evaluated by a combination of DNA techniques, mutagenesis, restriction mapping and subcloning. Results indicate that the preposed allelic replacement method is very useful for generating enterococcal pur and pyr auxotrophs which can be used infections caused by Enterococcus faecalis.

Rhodobacter sphaeroides strain 2.4.1deltaS mutagenized with a derivative of Tn5 produced eight UV-sensitive strains. Contour-clamped homogeneous electric field pulsed-field gel electrophoresis of the strains revealed at least five insertion sites in chromosome I, which were assumed to lack a DNA repair mechanism. DNA sequence analysis of these mutants confirmed a deficiency in three loci, which showed insertions to be within genes for subunits of the UV damage excision repair.

Restriction fragments produced by NotI, SfiI and SrfI formulated a physical map of the chromosome of Treponema pallidum subsp. pallidum (Nichols) of the length of approximately 1,030 to 1,080 kbp is size, which is the causative agent of syphilis. This restriction cleaved the T. pallidum genome in to 16,8 and 15 fragments. The process of construction of this physical map is discussed.

Auxotrophic mutants aid the analysis of the structure and function of chromosomes I and II of Rhodobacter sphaeroides 2.4.1T. The presence of histidine, thymine and p-aminobenzoic acid (pABA)-dihydroxybenzoic acid (dhBA) at low frequencies causes a return to prototrophy. Cosmids possessing the region of transposon location substitute the serine, uracil and pABA-dHBA mutants. The conclusions obtained from these experiments indicate a similarity among chromosomes in bacteria.

Approximately 10% of nonbacterial, sporadic diarrhea is caused by infection with astroviruses (1). Until 2008, astroviruses that infect humans were thought to be limited to 8 closely related serotypes. However, [...]

Amino acid requirements of Enterococcus faecalis OG1 are determined by a defined synthetic medium, which is used to reveal the unnecessary exogeneous purines or the pyrimidines that are absent. Genomic libraries prepared from strain OG1 are transduced into Escherichia coli auxotrophic mutants, and cloned DNAs with known functions are localized on the restriction map of OG1. The OG1 is generated using the SfiI, AscI and NotI fragments. The size of the OG1 chromosome is revised from the previous value of 2750kb to 2825kb.

The ColE1 plasmid cea gene codes for colicin E1, and is the first gene in an operon whose regulation is complex. The effects of anaerobiosis on the expression of cea was studied using cea-lacZ gene fusions. The results showed that the expression of cea increased by as much as 45-fold under anaerobic conditions. Both transcript and protein levels increased, indicating that the stimulation occured at a transcriptional level. The anaerobic expression of cea also required the SOS response, catabolite expression and the Fnr regulatory function.

A genetic map based on NotI restriction sites in Escherichia coli strain MG1655 was constructed. The NotI sites were placed on the genetic and physical map using several approaches which involved the use of transposons to introduce auxotrophic markers and NotI sites, Southern hybridization using NotI fragments as probes on an ordered lambda library, hybridization using known clones as probes on NotI digests and analysis of sequenced sites for NotI recognition sites. Comparisons of the derived map with maps of other E. coli strains showed some differences, but indicated an overall consistency.

Abstract Background Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references. Results In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3–4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported. Conclusions Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined.

Abstract Background Helicobacter canadensis is an emerging human pathogen and zoonotic agent. The genome of H. canadensis was sequenced previously and determined to contain 29 annotated coding regions associated with homopolymeric tracts. Results Twenty-one of the repeat-associated coding regions were determined to be potentially transcriptionally or translationally phase variable. In each case the homopolymeric tract was within the predicted promoter region or at the 5' end of the coding region, respectively. However, eight coding sequences were identified with simple sequence repeats toward the 3' end of the open reading frame. In these cases, the repeat tract would be too far into the coding region to be mediating translational phase variation. All of the 29 coding region-associated homopolymeric tracts display variability in tract length in the sequencing read data. Conclusions Twenty-nine coding regions have been identified in the genome sequence of Helicobacter canadensis strain NCTC13241 that show variations in homopolymeric tract length in the bacterial population, indicative of phase variation. Five of these are potentially associated with promoter regions, which would lead to transcriptional phase variation. Translational phase variation usually switches expression of a gene ON and OFF due to the repeat region being located sufficiently close to the initiation codon for the resulting frame-shift to lead to a premature termination codon and stop the translation of the protein. Sixteen of the 29 coding regions have homopolymeric tracts characteristic of translational phase variation. For eight coding sequences with repeats located later in the reading frame, changes in the repeat tract length would alter the protein sequence at the C-terminus but not stop the expression of the protein. This mechanism of C-terminal phase variation has implications for stochastic switching of protein sequence in bacterial species that already undergo transcriptional and translational phase variation.

Abstract Background We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. Results The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. Conclusion The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.

Abstract Background Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently. Results The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting sequence were filled with targeted dideoxy-terminators (DDT) sequencing and the sequence was confirmed by whole genome fingerprinting (WGF). When compared to the Nichols strain, 327 single nucleotide substitutions (224 transitions, 103 transversions), 14 deletions, and 18 insertions were found. On the proteome level, the highest frequency of amino acid-altering substitution polymorphisms was in novel genes, while the lowest was in housekeeping genes, as expected by their evolutionary conservation. Evidence was also found for hypervariable regions and multiple regions showing intrastrain heterogeneity in the T. pallidum chromosome. Conclusion The observed genetic changes do not have influence on the ability of Treponema pallidum to cause syphilitic infection, since both SS14 and Nichols are virulent in rabbit. However, this is the first assessment of the degree of variation between the two syphilis pathogens and paves the way for phylogenetic studies of this fascinating organism.

Abstract Background Community acquired (CA) methicillin-resistant Staphylococcus aureus (MRSA) increasingly causes disease worldwide. USA300 has emerged as the predominant clone causing superficial and invasive infections in children and adults in the USA. Epidemiological studies suggest that USA300 is more virulent than other CA-MRSA. The genetic determinants that render virulence and dominance to USA300 remain unclear. Results We sequenced the genomes of two pediatric USA300 isolates: one CA-MRSA and one CA-methicillin susceptible (MSSA), isolated at Texas Children's Hospital in Houston. DNA sequencing was performed by Sanger dideoxy whole genome shotgun (WGS) and 454 Life Sciences pyrosequencing strategies. The sequence of the USA300 MRSA strain was rigorously annotated. In USA300-MRSA 2658 chromosomal open reading frames were predicted and 3.1 and 27 kilobase (kb) plasmids were identified. USA300-MSSA contained a 20 kb plasmid with some homology to the 27 kb plasmid found in USA300-MRSA. Two regions found in US300-MRSA were absent in USA300-MSSA. One of these carried the arginine deiminase operon that appears to have been acquired from S. epidermidis. The USA300 sequence was aligned with other sequenced S. aureus genomes and regions unique to USA300 MRSA were identified. Conclusion USA300-MRSA is highly similar to other MRSA strains based on whole genome alignments and gene content, indicating that the differences in pathogenesis are due to subtle changes rather than to large-scale acquisition of virulence factor genes. The USA300 Houston isolate differs from another sequenced USA300 strain isolate, derived from a patient in San Francisco, in plasmid content and a number of sequence polymorphisms. Such differences will provide new insights into the evolution of pathogens.

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved — implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network — a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient's pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience. Here, the authors develop a genome evolution model to investigate the origin of functional redundancy in the human microbiome by analyzing its genomic content network and illustrate potential ecological and evolutionary processes that may contribute to its resilience. [ABSTRACT FROM AUTHOR]

Recent studies using mouse models suggest that interaction between the gut microbiome and IL-17/IL-22-producing cells plays a role in the development of metabolic diseases. We investigated this relationship in humans using data from the prediabetes study of the Integrated Human Microbiome Project (iHMP). Specifically, we addressed the hypothesis that early in the onset of metabolic diseases there is a decline in serum levels of IL-17/IL-22, with concomitant changes in the gut microbiome. Clustering iHMP study participants on the basis of longitudinal IL-17/IL-22 profiles identified discrete groups. Individuals distinguished by low levels of IL-17/IL-22 were linked to established markers of metabolic disease, including insulin sensitivity. These individuals also displayed gut microbiome dysbiosis, characterized by decreased diversity, and IL-17/IL-22-related declines in the phylum Firmicutes, class Clostridia, and order Clostridiales This ancillary analysis of the iHMP data therefore supports a link between the gut microbiome, IL-17/IL-22, and the onset of metabolic diseases. This raises the possibility for novel, microbiome-related therapeutic targets that may effectively alleviate metabolic diseases in humans as they do in animal models. [ABSTRACT FROM AUTHOR]