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International Journal of Translational Medicine (IJTM). Bacterial identification result by Sanger
sequencing. Therefore, we propose an efficient system in various fields requiring rapid quantification
of indicator microorganisms, such as medicine, agriculture, and marine biology, etc. Through parallel
comparison analysis, it was confirmed that the qRT-PCR technique could be an excellent alternative
to existing NGS-based 16S V3-V4 metagenome sequencing methods, as it could enable reliable
detection and quantification (for the gut-associated microbiota: Akkermansia, Bacteroides,
Bifidobacterium, Phascolarctobacterium, and Roseburia ). This difference has profound
consequences on the development of the immune system, as highlighted by a recent study that
compared mice housed in SPF conditions with mice co-housed with pet store mice and found that
the lack of pathogen experience has major effects on the cellular composition of the innate and
adaptive immune systems, especially failing to elicit effector-differentiated and mucosally distributed
memory T cells ( 145 ). Chapter 5 Identification of Gram-Positive Organisms.. 53. Molecular
Microciology Laboratory Department of Biochemistry. An SLE-associated DNASE1L3
polymorphism (R206C) was also shown to have reduced DNase activity ( 135, 136 ).
Characterization of IdLNF1-specific T cell clones from the (NZB x SWR)F1 murine model for
systemic lupus erythematosus. You can write your entire paper as per the Microbiology Research
guidelines and auto format it. Fueling the fire with fibers: bacterial amyloids promote inflammatory
disorders. A study of 7,326 patients newly diagnosed with SLE showed that the occurrence of three
or more infection-related hospitalizations greatly increased risk of end-stage renal disease (ESRD),
indicating an effect of infections on SLE disease activity ( 75 ). The role of defective clearance of
apoptotic cells in systemic autoimmunity. In addition, we selected five amplicon samples with the
high- and low-frequencies generated after qRT-PCR amplification, respectively, and conducted
Sanger validation to evaluate the accuracy and sensitivity of the designed genus-specific primers.
This supports the concept that cross-reactivity may occur in susceptible individuals with colonization
by autoantigen ortholog-producing bacteria. CpG motifs present in bacteria DNA rapidly induce
lymphocytes to secrete interleukin 6, interleukin 12, and interferon gamma. Using stool samples
obtained from 100 healthy adults, we performed a comparative analysis to evaluate the accuracy of
microbial quantification by two different molecular technologies. ( a ) The overall experimental
workflow of the qRT-PCR assay and NGS-based 16S V3-V4 metagenome sequencing. ( b )
Schematic diagram showing the process to design the genus-specific primer set to quantify the
proportions of the five selected bacterial genera within each sample using qRT-PCR. The primer
sequences were as follows: 16S 341F forward primer is 5?-
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3. We found
that curli can fibrilize with eukaryotic DNA as well, suggesting that bacterial amyloids can not only
expose the immune system to bacterial DNA, but also bind and render the host DNA immunogenic (
30 ). The MPN method can also be referred to as the multiple tube fermen-. HPV and systemic lupus
erythematosus: a mosaic of potential crossreactions. Immunopathogenesis and spectrum of infections
in systemic lupus erythematosus. Pathological amyloids, which are generally associated with
neurodegenerative disease, such as Alzheimer's or Parkinson's disease, are the result of protein
misfolding and are cytotoxic for the host that produces them. Also see PART XIV: USMLE
(National Board) Practice Examination starting on page 731. It is a fill-in-the-blank activity that
features twenty-six microbiology terms. Multiple overlaid connected line graphs show the
quantitative identity of each bacterial genus measured by both methods. SLE patients were found to
have higher prevalence of periodontal disease at younger age than healthy controls, with severe
forms of periodontitis and changes in the oral microbiota characterized by decreased species
diversity and higher bacterial loads, which were linked to increasing local production of pro-
inflammatory cytokines ( 199, 200 ), highlighting a role for the oral microbiome in the pathogenesis
of lupus. The 16S rRNA gene (approximately 1500 bp) consists of the nine hyper-variable regions
(V1-V9) interspersed among highly conserved sequences. Farmingdale, New York National Farm
Medicine Center. Our findings showed that relative bacterial proportions of five genera within
samples measured via qRT-PCR performed under normalized mDNA concentration conditions were
statistically similar to those based on 16S metagenome sequencing data.
Swiss Federal Institute of Technology Mark S. Peppler. The use, distribution or reproduction in other
forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that
the original publication in this journal is cited, in accordance with accepted academic practice.
Tropical Medicine and Infectious Disease (TropicalMed). The same techniques can be used to test
microbial DNA in the blood during infections and sepsis, and very recently an analytical and clinical
validation of a next-generation sequencing test, which can identify and quantify microbial cell-free
DNA in the plasma of patients with and without sepsis, has demonstrated the feasibility to detect in
plasma the circulating free DNA of 1,250 clinically relevant bacteria, DNA viruses, fungi, and
eukaryotic parasites ( 122 ). If Escherichia coli is used, the 0.5 McFarland standard is equivalent.
Then, additional PCR amplification was performed to add multiplexing indices and Illumina
sequencing adapters using the Nextera XT Index Kit (Illumina, San Diego, CA, USA). Article types
Author guidelines Editor guidelines Publishing fees Submission checklist Contact editorial office
Submit your research Search Download article. One common approach is to use the broth dilution
method, wherein a. In the United States, the EPA regulates disinfectants. Funding This research
received no external funding. Typhimurium that cannot produce curli—and therefore cannot generate
biofilms—still developed autoantibodies ( 30, 196 ), albeit at a much lower level than those infected
with Salmonella that could produce curli. Consistent with findings that germ-free conditions do not
influence disease outcome ( 93 ), treating lupus-prone mice with antibiotics from the time of weaning
also did not impact disease activity. Direct count methods are used in the areas of food,132, 133
biocidal,134, 135 metal working fluids,136. This is an open-access article distributed under the terms
of the Creative Commons Attribution License (CC BY). This author is willing to donate free copies
of their book in exchange for reviews (if circumstances allow) and the knowledge that their book is
being read and enjoyed. Printed in the United States of America on acid-free paper. Journal of
Cardiovascular Development and Disease (JCDD). Pyroptosis is canonically dependent on the
protease caspase 1, making this process inherently inflammatory. A colony PCR amplification using
the M13 primer pair (M13F: 5?-GTAAAACGACGGCCAG-3?; M13R: 5?-
CAGGAAACAGCTATGAC-3?) was conducted to check whether the target sequence was inserted
in the plasmid cloning vector. Chapter 20 Microbiological and Clinical Aspects of the Pathogenic
Spirochetes. 249. Gut microbiota in human systemic lupus erythematosus and a mouse model of
lupus. It remains to be determined whether clinical or subclinical infections are fueling NETosis, and
whether genetic or environmental factors cause the increased propensity of NETting in SLE patients.
Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic
sequencing. The MPN method is useful in the estimation of low microorganism counts where
particulate mat-. Bloomberg School of Public Health University of Maryland School of Medicine.
How these nuclear molecules become available to the immune system for recognition, presentation,
and targeting is an area of research where complexities remain to be disentangled. The antigen in the
vaccine is the same as the antigen on the surface of the disease-causing microbe. As mentioned
above, bacterial infections are well-known triggers of pyroptosis ( 33 ), and common pathogens in
SLE patients including E. An example, especially important for researchers working with mouse
models of lupus, is the acidification of water that was found to decrease the levels of autoantibodies
and delay the onset of nephritis in lupus-prone mice ( 96 ) while augmenting the presence of
Lactobacillus reuteri, belonging to the phylum of Firmicutes. As a result of 16S metagenome
sequencing, the average number of demultiplexed reads generated from 100 samples was 133,288, of
which 65,892 were filtered through the DADA2 pipeline with non-chimeric reads ( Supplementary
Table S1 ).
A Changing Ecosystem across Age, Environment, Diet, and Diseases. The regulation of disinfectants
and antiseptics falls under the jurisdiction of different agencies. Commensal orthologs of the human
autoantigen Ro60 as triggers of autoimmunity in lupus. Interleukin-18 regulates both Th1 and Th2
responses. Indeed, many companies and researchers involved in microbial molecular diagnosis are
attempting to overcome the issue of high-sequence similarity between bacterial species arising from
16S rRNA gene sequencing by developing specific primer pairs for use in qRT-PCR. Such binding
accelerates the fibrillation of the amyloid and protects the DNA from degradation by DNases ( 30 ).
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles
during periods of human health and disease. Periodontal disease in Chinese patients with systemic
lupus erythematosus. International Journal of Environmental Research and Public Health (IJERPH).
Few of these factors include review board, rejection rates, frequency of inclusion in indexes, and
Eigenfactor. The injection of bacterial DNA induced anti-dsDNA autoAbs by the same mechanism (
215 ), and the report that mammalian DNA did not elicit the same result can be explained by the fact
that genomic mammalian DNA is not as immunogenic as bacterial DNA, especially if the latter is
complexed to a TLR2 ligand like curli or another amyloid ( 32 ). Tropical Medicine and Infectious
Disease (TropicalMed). In this respect, we claim that the qRT-PCR method is one of appropriate
tools for identifying the relative proportions of particular microorganisms within a sample. In this
study, we investigated the concordance between qRT-PCR and NGS technology to confirm the
efficiency of microbial quantification at the genus level associated with human health. Finally, we
conducted an in silico test using the NCBI Nucleotide BLAST web tool to validate the bacterial
genus-specificities of five primer pairs designed for this study ( Supplementary Figure S1 ). The
human intestinal microbiome in health and disease. Sterilization is the removal of all microbes,
including endospores, and can be achieved by mechani-. Analysis of plasma Epstein-barr virus DNA
to screen for nasopharyngeal cancer. MPN method have also been developed to further expand the
use of the standard MPN method to. Development of autoantibodies before the clinical onset of
systemic lupus erythematosus. When caspase 1 is activated, gasdermin-D rapidly forms pores in the
plasma membrane, allowing for osmotic lysis and release of inflammatory cytokines and cell
contents, in contrast to the non-inflammatory apoptosis. Each summary table ( Supplementary Table
S6 ), which included the Ct value of five bacterial genera, was used to compare NGS-based bacterial
frequency data. 2.6. Sanger Sequencing The Sanger sequencing was conducted to verify the
molecular specificity and experimental accuracy of the five primer pairs designed for this study.
Systemic lupus erythematosus-like autoimmune abnormalities induced by bacterial infection. SLE
patients were found to have higher prevalence of periodontal disease at younger age than healthy
controls, with severe forms of periodontitis and changes in the oral microbiota characterized by
decreased species diversity and higher bacterial loads, which were linked to increasing local
production of pro-inflammatory cytokines ( 199, 200 ), highlighting a role for the oral microbiome in
the pathogenesis of lupus. You can write your entire paper as per the Microbiology Research
guidelines and auto format it. This difference has profound consequences on the development of the
immune system, as highlighted by a recent study that compared mice housed in SPF conditions with
mice co-housed with pet store mice and found that the lack of pathogen experience has major effects
on the cellular composition of the innate and adaptive immune systems, especially failing to elicit
effector-differentiated and mucosally distributed memory T cells ( 145 ). University of Maryland
School of Medicine Juelich, Germany. If Escherichia coli is used, the 0.5 McFarland standard is
equivalent. For example, an organism formerly known as Pseudomonas cepacia has been reclassified
as Burkholderia cepacia because the base sequence of its DNA was found to be significantly
different from the DNA of the members of the genus Pseudomonas. Notably, the development of
antinuclear antibodies specific for nucleic acids, arguably the hallmark of SLE, has been linked with
bacterial infections in both humans and mice.
Please let us know what you think of our products and services. HPV and systemic lupus
erythematosus: a mosaic of potential crossreactions. The role of cell death in the pathogenesis of
SLE: is pyroptosis the missing link. The human experiment in this study (samples collection) was
approved by the ethics committee of Theragen Bio (Theragen Bio, South Korea) Institutional
Review Board (IRB Protocol Number: 700062-20180905-JR-005-01). Multiple overlaid connected
line graphs show the quantitative identity of each bacterial genus measured by both methods.
Inherited classical and alternative pathway complement deficiencies in children: a single center
experience. Vaccines are made from microbes that are dead or inactive so that they are unable to
cause the disease. Through a very simple and fun lesson, Rebecca begins to instill the benefits and
necessities of good hygiene, but also avoids making bacteria into a scary monster. Idiotope-specific
T cell clones that recognize syngeneic immunoglobulin fragments in the context of class II molecules.
We highlight that four bacterial ( Akkermansia, Bifidobacterium, Phascolarctobacterium, and
Roseburia ) genera present in low proportions in 100 samples of human gut microbiota also showed
significant relative proportions in quantification results. Bacterial amyloids: the link between
bacterial infections and autoimmunity. Dysregulation of germinal centres in autoimmune disease.
Comparative rates of serious infections among patients with systemic lupus erythematosus receiving
immunosuppressive medications. Be sure to tell the author who you are, what organization you are
with, how many books you need, how they will be used, and the number of reviews, if any, you
would be able to provide. Using stool samples obtained from 100 healthy adults, we performed a
comparative analysis to evaluate the accuracy of microbial quantification by two different molecular
technologies. ( a ) The overall experimental workflow of the qRT-PCR assay and NGS-based 16S
V3-V4 metagenome sequencing. ( b ) Schematic diagram showing the process to design the genus-
specific primer set to quantify the proportions of the five selected bacterial genera within each
sample using qRT-PCR. The highest levels were observed in class V membranous nephritis, in which
they correlated with complement deposition, suggesting that the release of HMGB1 in the urine is
not only due to passive excretion secondary to elevated proteinuria, but is likely linked to a
mechanism inherent to class V disease ( 166 ). Identification of a new putative functional IL18 gene
variant through an association study in systemic lupus erythematosus. Jeong J, Mun S, Oh Y, Cho C-
S, Yun K, Ahn Y, Chung W-H, Lim MY, Lee KE, Hwang TS. Infections can be a source of
extracellular nuclear antigens because they expose nucleic acids derived from bacteria and especially
from bacterial biofilms, which are very rich in bacterial DNA and amyloids carrying extracellular
DNA. First of all, double-stranded DNA concentration within all mDNA samples was measured
using the Qbit Fluorometer 4.0 v at the Center for Bio-medical Engineering Core Facility (Dankook
University, Yongin, Korea) and 1X dsDNA HS Assay kit (ThermoFisher Scientific, Waltham, MA,
USA). To select bacterial genera for quantifying their frequencies in the specimens, we successfully
prepared the Illumina 16S V3-V4 short-read amplicon sequencing libraries using these 100 mDNA
samples. Additionally, we verified an association between bacterial proportions data measured with
two different quantification methods using the Spearman correlation statistical analysis to
supplement these parallel comparison results. Jaypee Brothers Medical Publishers Pvt Ltd.,2009,
668. Many bacterial models have been reported to activate the inflammasome and induce pyroptosis,
from Salmonella ssp ( 155, 156 ) to Francisella novicida ( 157 ), Streptocuccus pneumoniae ( 158 ),
and Listeria monocytogenes ( 159 ). As mentioned above, bacterial infections are well-known
triggers of pyroptosis ( 33 ), and common pathogens in SLE patients including E. Therefore, these
results suggest that the defects in phagocytosis are either limited to a few patients or are not
genetically determined but rather may be secondary to immunosuppressive therapies, infections or a
prolonged inflammatory state. Many bacterial PAMPs can trigger cytoplasmic PRRs like AIM2 and
NLRPs, which are upstream of the inflammasome and the downstream caspases, and their activation
leads to secretion of caspase 1-dependent cytokines IL-1b and IL-18 ( 154 ). The table below
indicates the level of access a journal has as per Sherpa Romeo's archiving policy. The best studied
bacterial amyloid is curli, produced by enteric bacteria that commonly cause infections in SLE
patients, including Escherichia coli and Salmonella spps. Editor’s Choice articles are based on
recommendations by the scientific editors of MDPI journals from around the world.
In this respect, we claim that the qRT-PCR method is one of appropriate tools for identifying the
relative proportions of particular microorganisms within a sample. Wayne State University School of
Medicine Department of Biomedical Sciences. The first edition of the Practical Handbook of
Microbiology was published in 1989. Human TLR9 confers responsiveness to bacterial DNA via
species-specific CpG motif recognition. Moreover, infections can release host nucleic acids in the
extracellular compartment because of the different types of cell death that can occur during infection,
either as a direct cytotoxicity of the pathogen or as a consequence of normal immune responses,
notably pyroptosis ( 33 ) and the extrusion of neutrophil extracellular traps (NETs) ( 11, 34 ). Human
parvovirus B19 infection: its relationship with systemic lupus erythematosus. Impact of dietary
deviation on disease progression and gut microbiome composition in lupus-prone SNF1 mice. Our
findings showed that relative bacterial proportions of five genera within samples measured via qRT-
PCR performed under normalized mDNA concentration conditions were statistically similar to those
based on 16S metagenome sequencing data. Gout, Urate, and Crystal Deposition Disease (GUCDD).
Chapter 21 The Genus Vibrio and Related Genera. 267. When LPS is recognized in the cytoplasm by
caspase 4 or 5 in humans (caspase 11 in mice), caspase 1-independent pyroptosis is also initiated. The
Sanger sequencing with purified products as template DNA was carried out using the ABI 3500XL
Genetic Analyzer sequencer (ThermoFisher Scientific, Waltham, MA, USA) at the Center for Bio-
medical Engineering Core Facility (Dankook University, Yongin, Korea). The author will provide you
with a free copy of their book in exchange for an honest review. Most of the contributors to the first
edition were no longer. Department of Microbiology and Immunology Research Centre Juelich.
These techniques are used in the clinic for non-invasive prenatal genetic testing ( 118 ) or cancer
liquid biopsies, which can detect asymptomatic tumors and cancer-associated mutations ( 119, 120 ).
The organism of significance whose retention on the filter is most. Intestinal dysbiosis is associated
with altered short-chain fatty acids and serum-free fatty acids in systemic lupus erythematosus. If
any copyright material has not been acknowledged please write and let us know so we may.
Cutaneous manifestations of neonatal lupus and risk of subsequent congenital heart block.
Richmond, University of Massachusetts Medical School, United States Marko Radic, University of
Tennessee College of Medicine, United States. You and the author will discuss what sites you will
post your review to and what kind of copy of the book you would like to receive (eBook, PDF,
Word, paperback, etc.). To begin, click the purple email icon to send this author a private email. A
diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity. The
turbidimetric reading instrument can be, for example, the spec-. Netting neutrophils are major
inducers of type I IFN production in pediatric systemic lupus erythematosus. Bacteria were
characterized by form as being yeast, streptobacilli, bacilli. Very recent evidence supports a role for
biofilm-forming infections in SLE pathogenesis. The vaccine stimulates the body to produce
antibodies against the antigen in the vaccine. Together, this model suggests that there is selective
cross-reactivity between a Ro60 ortholog from commensal bacteria and human Ro60, further
emphasizing how infection may play a role in triggering autoimmunity in lupus ( 223 ). Clinical
studies have shown that patients with SLE who had infection-related hospitalizations suffer a
profoundly increased risk of end-stage renal disease, suggesting that infections have an effect on
SLE disease activity ( 74, 75 ).
You need to assess all these factors before you make your final call. Playful, educational and vibrant,
Meet Bacteria is a great way to start your child on the road to learning about nature and the
numerous fascinating aspects of the world around us. An SLE-associated DNASE1L3 polymorphism
(R206C) was also shown to have reduced DNase activity ( 135, 136 ). Trademark Notice: Product or
corporate names may be trademarks or registered trademarks, and are used only for. The human
intestinal microbiome in health and disease. Farmingdale State College Yale University School of
Medicine. The authors and publishers have attempted to trace the copyright. Risk factors for drug-
resistant bloodstream infections in patients with systemic lupus erythematosus. Impaired uptake of
apoptotic cells into tingible body macrophages in germinal centers of patients with systemic lupus
erythematosus. When enough people are vaccinated against a disease it is possible for that disease to
be eliminated from the world e.g. in 1980 The World Health Organization announced that smallpox
had been eradicated. Chapter 13 Bacterial Cell Wall: Morphology and Biochemistry. 159. In this
review, we present findings from recent literature highlighting a role for bacterial infections and
bacterial biofilms in the extracellular exposure of nuclear autoAgs, and their ability to stimulate the
autoreactive immune responses in SLE ( Figure 1 ). Editors select a small number of articles recently
published in the journal that they believe will be particularly. The Integrative Human Microbiome
Project: dynamic analysis of microbiome-host omics profiles during periods of human health and
disease. The compartmentalization of endogenous nucleic acids and PRRs usually prevents the
inappropriate stimulation of the immune system by these potent danger signals in absence of
infections ( 15 ). Typhimurium that cannot produce curli—and therefore cannot generate
biofilms—still developed autoantibodies ( 30, 196 ), albeit at a much lower level than those infected
with Salmonella that could produce curli. York Institute of Technology and to business students at
the State University of New York at Stony. Average standard curve calculation results using qRT-
PCR assay. Curli fibers are highly conserved between Salmonella typhimurium and Escherichia coli
with respect to operon structure and regulation. Direct count methods are used in the areas of
food,132, 133 biocidal,134, 135 metal working fluids,136. International Standard Book Number-13:
978-0-8493-9365-5 (Hardcover). Statistical result of the Spearman correlation test between two
different quantification methods. This is supported by reports of high levels of circulating endotoxin
and more frequent bacteremia in SLE patients ( 68, 69, 89, 104 ). The highest levels were observed
in class V membranous nephritis, in which they correlated with complement deposition, suggesting
that the release of HMGB1 in the urine is not only due to passive excretion secondary to elevated
proteinuria, but is likely linked to a mechanism inherent to class V disease ( 166 ). As a consequence,
mast cells migrate in the site of infection and worsen the damage to the barrier function of bladder
urothelium ( 160 ). The bar plot shown on the left side represents an average abundance of the five
bacterial genera calculated from 16S metagenomic profiling analysis. Therefore, we reselected the
transaldolase and D-alanine D-alanine ligase ( ddl ) genes as target-specific genes for
Bifidobacterium and Akkermansia, respectively. Chapter 3 Culturing and Preserving
Microorganisms.. 31. From 2001 until 2004 he was a member of the Advisory Com-. His long-term
interest is the use of technology in the development of commercial products. He also.