Placental Microbiome: a Paradigm Shift or Flaw in the Methodology?

2021 ◽  
Vol 76 (5) ◽  
pp. 436-448
Author(s):  
Elena V. Shipitsyna

Rapid development of high-throughput DNA sequencing technologies and bioinformatics methods, together with a substantial reduction of their cost, have provided tremendous opportunities for studying the human microbiome. In recent years, much attention has been paid to studies of the microbiome of the upper reproductive tract of woman and the fetoplacental system, which have traditionally been considered sterile. Obtaining irrefutable evidence of the existence of the placental microbiome would enable us to believe with a high degree of certainty that microorganisms colonize the fetus already in the womb, which would have far-reaching consequences not only for medicine, but also for basic biology. This issue triggered a heated discussion among microbiologists, molecular biologists, obstetricians, and neonatologists. In the past few years, a number of studies have been published, both refuting and confirming the dogma, accepted for many decades, that the placenta and fetus are sterile during a healthy pregnancy. This literature review is a critical analysis of the results of studies into the placental microbiome. It provides arguments both for supporters of the hypothesis of the resident microbiota of the placenta and their opponents. Particular attention is paid to the methodological requirements for molecular studies of biological material with low microbial biomass, compliance with which is crucial for obtaining reliable results.

Author(s):  
Hye-Won Cho ◽  
Yong-Bin Eom

High-throughput DNA sequencing technologies have facilitated the in silico forensic analysis of human microbiome. Specific microbial species or communities obtained from the crime scene provide evidence of human contacts and their body fluids. The microbial community is influenced by geographic, ethnic, lifestyle, and environmental factors such as urbanization. An understanding of the effects of these external stressors on the human microbiome and determination of stable and changing elements are important in selecting appropriate targets for investigation. In this study, the Forensic Microbiome Database (FMD) (http://www.fmd.jcvi.org) containing the microbiome data of various locations in the human body in 35 countries was used. We focused on skin, saliva, vaginal fluid, and stool and found that the microbiome distribution differed according to the body part as well as the geographic location. In the case of skin samples, Staphylococcus species were higher than Corynebacterium species among Asians compared with Americans. Holdemanella and Fusobacterium were specific in the saliva of Koreans and Japanese populations. Lactobacillus was found in the vaginal fluids of individuals in all countries, whereas Serratia and Enterobacter were endemic to Bolivia and Congo, respectively. This study is the first attempt to collate and describe the observed variation in microbiomes from the forensic microbiome database. As additional microbiome databases are reported by studies worldwide, the diversity of the applications may exceed and expand beyond the initial identification of the host.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1029.1-1029
Author(s):  
Y. Livshits ◽  
O. Teplyakova ◽  
A. Sarapulova

Background:Telemedicine counseling (TMC) has gained rapid development during the COVID-19 pandemic. The prospect of using this technology in rheumatology was based on the possibility of getting maximum information about the patient during the survey, examination and interpretation of laboratory and instrumental data, that is excepting direct contact with the patient. Several rheumatological clinics have reported on the success of using TMC. However, there is very little data of the difficulties that can be encountered when organizing this process.Objectives:To characterize the identified problems during TMC in rheumatology, to suggest potential directions for their elimination.Methods:Since June 2021, on the basis of the Medical Association “New Hospital”, Yekaterinburg, Russian Federation, 76 TMCs have been performed on the profile of rheumatology in patients aged 29 to 71 years. Of these, 13 applied to the primary TMC, the other patients were preliminarily examined in person. The consultation included the preliminary acquaintance with the examination results, a 20-minute video communication and writing of a conclusion. After each TMC, a survey was conducted between the doctor and the patient, including the identified deficiencies in counseling. The frequency of identified problems is presented as an absolute indicator and as a percentage of the total number of TMCs performed.Results:We noted a high degree of patient satisfaction: 74 (97.4%) responded that they received answers to all. However, according to the doctor, the following groups of problems were identified.[1]Technical problems in 29 (38.2%): most often there were various problems with the Internet, but there were also registered: the end of the charge on the patient’s tablet, the patient was not registered in the electronic queue. Elimination of these violations depends on the work of IT-specialists, but each consulting physician should be prepared for an immediate transition to an alternative form of communication (for example - telephone).[2]Lack of objective examination, leading to the impossibility of correct remote diagnosis - 8 (10.5%). This problem was identified due to the inability to establish the presence or absence of arthritis during the initial diagnosis (6 cases) and to clarify the nature of the rash (2 cases). All patients are invited for a face-to-face consultation.[3]The need to write prescriptions for psychotropic drugs - 12 (15.8%), which under the conditions of national legislation cannot be done in the TMC regime.[4]The time spent directly on remote communication with the patient was 17.2 minutes (from 8 to 31), however, taking into account the study data and writing the conclusion, the total time was 40.7 minutes (from 21 to 73). Thus, it turned out that the average time for remote and face-to-face consultations is the same, while TMC’s payment is only about 50% of the face-to-face consultation. This situation reduces the doctor’s interest in carrying out TMC. The solution to the problem is associated with reducing the time for the documentation process through technical improvements. In addition, of the 9 patients in whom the TMC process lasted 60 minutes or more, 5 were diagnosed with fibromyalgia. It is possible that with a previously established diagnosis of fibromyalgia, only face-to-face counseling should be recommended to patients.Conclusion:The TMC system is promising, however, there are a number of problems that need to be improved, since they can reduce the doctor’s interest in using this technology.Disclosure of Interests:None declared


Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 65
Author(s):  
Patricia Haug ◽  
Samuel Koller ◽  
Jordi Maggi ◽  
Elena Lang ◽  
Silke Feil ◽  
...  

Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.


2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Silvio Garofalo ◽  
Marisa Cornacchione ◽  
Alfonso Di Costanzo

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.


Author(s):  
Anthony Merle ◽  
P. F. Ehlers

Pipeline stress-corrosion cracking (SCC) is an ongoing integrity concern for pipeline operators. A number of different strategies are currently employed to locate and mitigate SCC. Ultrasonic in-line inspection tools have proven capable of locating SCC, but reliability of these tools in gas pipelines remains in question. Rotating hydrotest programs are effectively employed by some companies but may not provide useful information as to the location of SCC along the pipeline. NACE Standard RP0204-2004 (SCC Direct Assessment Methodology) outlines factors to consider and methodologies to employ to predict where SCC is likely to occur, but even this document acknowledges that there are no well-established methods for predicting the presence of SCC with a high degree of certainty. Predictive modelling attempts to date have focused on establishing quantitative relationships between environmental factors and SCC formation and growth; these models have achieved varying degrees of success. A statistical approach to SCC predictive modelling has been developed. In contrast to previous models that attempted to determine direct correlations between environmental parameters and SCC, the new model statistically analyzed data from dig sites where SCC was and was not found. Regression techniques were used to create a multi-variable logistic regression model. The model was applied to the entire pipeline and verification digs were performed. The dig results indicated that the model was able to predict locations of SCC along the pipeline.


2016 ◽  
Author(s):  
Justin D Silverman ◽  
Alex Washburne ◽  
Sayan Mukherjee ◽  
Lawrence A David

ABSTRACTHigh-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbiota surveys reflect the relative abundance of bacterial taxa and not their absolute levels. It is well known that applying common statistical methods, such as correlation or hypothesis testing, to relative abundance data can lead to spurious results. Here, we introduce the PhILR transform, a data transform that utilizes microbial phylogenetic information. This transform enables off-the-shelf statistical tools to be applied to microbiota surveys free from artifacts usually associated with analysis of relative abundance data. Using environmental and human-associated microbial community datasets as benchmarks, we find that the PhILR transform significantly improves the performance of distance-based and machine learning-based statistics, boosting the accuracy of widely used algorithms on reference benchmarks by 90%. Because the PhILR transform relies on bacterial phylogenies, statistics applied in the PhILR coordinate system are also framed within an evolutionary perspective. Regression on PhILR transformed human microbiota data identified evolutionarily neighboring bacterial clades that may have differentiated to adapt to distinct body sites. Variance statistics showed that the degree of covariation of bacterial clades across human body sites tended to increase with phylogenetic relatedness between clades. These findings support the hypothesis that environmental selection, not competition between bacteria, plays a dominant role in structuring human-associated microbial communities.


2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.


2014 ◽  
Vol 67 (2) ◽  
pp. 7247-7260 ◽  
Author(s):  
Pablo Andrés Gutiérrez Sánchez ◽  
Juan Fernando Alzate ◽  
Mauricio Marín Montoya

Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants.


2021 ◽  
Vol 111 (1) ◽  
pp. 8-11
Author(s):  
Remco Stam ◽  
Pierre Gladieux ◽  
Boris A. Vinatzer ◽  
Erica M. Goss ◽  
Neha Potnis ◽  
...  

Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue . Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.


Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 858 ◽  
Author(s):  
Krehenwinkel ◽  
Pomerantz ◽  
Prost

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.


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