keyword
https://read.qxmd.com/read/37988265/improving-species-level-taxonomic-assignment-from-16s-rrna-sequencing-technologies
#21
JOURNAL ARTICLE
David Bars-Cortina, Ferran Moratalla-Navarro, Ainhoa García-Serrano, Núria Mach, Lois Riobó-Mayo, Jordi Vea-Barbany, Blanca Rius-Sansalvador, Silvia Murcia, Mireia Obón-Santacana, Victor Moreno
Analysis of the bacterial community from a 16S rRNA gene sequencing technologies requires comparing the reads to a reference database. The challenging task involved in annotation relies on the currently available tools and 16S rRNA databases: SILVA, Greengenes and RDP. A successful annotation depends on the quality of the database. For instance, Greengenes and RDP have not been updated since 2013 and 2016, respectively. In addition, the nature of 16S sequencing technologies (short reads) focuses mainly on the V3-V4 hypervariable region sequencing and hinders the species assignment, in contrast to whole shotgun metagenome sequencing...
November 2023: Current protocols
https://read.qxmd.com/read/37955334/cutaneous-vasculitis-in-autoinflammatory-diseases
#22
REVIEW
Ko-Ron Chen
Autoinflammatory diseases (AIDs) characterized by recurrent episodes of localized or systemic inflammation are disorders of the innate immune system. Skin lesions are commonly found in AIDs and cutaneous vasculitis can coexist with AIDs and even present as the most striking feature. This review aims to focus on the frequent cutaneous vasculitis association in three monogenic AIDs including familial Mediterranean fever (FMF), deficiency of adenosine deaminase type 2 (DADA2), and the recently identified adult-onset VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome...
November 13, 2023: Journal of Dermatology
https://read.qxmd.com/read/37848905/efficacy-and-safety-of-thalidomide-in-children-with-monogenic-autoinflammatory-diseases-a-single-center-real-world-evidence-study
#23
JOURNAL ARTICLE
Caihui Zhang, Zhongxun Yu, Sihao Gao, Mingsheng Ma, Lijuan Gou, Changyan Wang, Lin Wang, Ji Li, Linqing Zhong, Yu Zhou, Wei Wang, Hongmei Song
BACKGROUND: Monogenic autoinflammatory diseases (AIDs) are rare inflammatory diseases caused by genetic variants. The pathogenesis is complex and treatment options are limited. This study aimed to describe the safety and efficacy of thalidomide in the treatment of monogenic AIDs. METHODS: This was a single-center, single-arm, real-world study. From September 2016 to August 2021, patients with monogenic AIDs who met the inclusion and exclusion criteria were given thalidomide for 12 months...
October 17, 2023: Pediatric Rheumatology Online Journal
https://read.qxmd.com/read/37823280/microbiome-depiction-through-user-adapted-bioinformatic-pipelines-and-parameters
#24
JOURNAL ARTICLE
Eric I Nayman, Brooke A Schwartz, Fantaysia C Polanco, Alexandra K Firek, Alayna C Gumabong, Nolan J Hofstee, Giri Narasimhan, Trevor Cickovski, Kalai Mathee
Introduction. The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility. In microbial compositional analysis, there is a growing recognition for the need to move away from a one-size-fits-all approach to data processing. Gap Statement. Few evidence-based recommendations exist for setting parameters of programs that infer microbiota community profiles despite these parameters significantly impacting the accuracy of taxonomic inference...
October 2023: Journal of Medical Microbiology
https://read.qxmd.com/read/37821648/role-of-microbiome-in-the-outcomes-following-surgical-repair-of-perianal-fistula-prospective-cohort-study-design-and-preliminary-results
#25
JOURNAL ARTICLE
Marco Bertucci Zoccali, Dalia H Moallem, Heekuk Park, Anne-Catrin Uhlemann, James M Church, Ravi P Kiran
BACKGROUND: Anal fistulae are common, predominantly cryptoglandular, and almost invariably require surgical treatment. Recurrences are common for procedures other than fistulotomy regardless of technique and adequacy of repair. Growing evidence supports the pivotal role of specific intestinal bacteria in anastomotic failures after bowel resection. Anal crypts harbor colonic microbiota suggesting that similar mechanisms to anastomotic healing might prevail after anal fistula repair and hence influence healing...
October 11, 2023: World Journal of Surgery
https://read.qxmd.com/read/37821195/deficiency-of-adenosine-deaminase-2-clinical-manifestations-diagnosis-and-treatment
#26
REVIEW
Andrew Grim, Keila R Veiga, Nadine Saad
Deficiency of adenosine deaminase 2 (DADA2) is a monogenic vasculitis syndrome caused by biallelic mutations in the adenosine deaminase 2 gene. The diagnosis of DADA2 is confirmed by decreased enzymatic activity of ADA2 and genetic testing. Symptoms range from cutaneous vasculitis and polyarteritis nodosa-like lesions to stroke. The vasculopathy of DADA2 can affect many organ systems, including the gastrointestinal and renal systems. Hematologic manifestations occur early with hypogammaglobulinemia, lymphopenia, pure red cell aplasia, or pancytopenia...
November 2023: Rheumatic Diseases Clinics of North America
https://read.qxmd.com/read/37813636/a-streamlined-pipeline-based-on-hmmufotu-for-microbial-community-profiling-using-16s-rrna-amplicon-sequencing
#27
JOURNAL ARTICLE
Hyeonwoo Kim, Jiwon Kim, Ji Won Choi, Kwang-Sung Ahn, Dong-Il Park, Sangsoo Kim
Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment...
September 2023: Genomics & Informatics
https://read.qxmd.com/read/37810879/a-two-cohort-study-on-the-association-between-the-gut-microbiota-and-bone-density-microarchitecture-and-strength
#28
JOURNAL ARTICLE
Paul C Okoro, Eric S Orwoll, Curtis Huttenhower, Xochitl Morgan, Thomas M Kuntz, Lauren J McIver, Alyssa B Dufour, Mary L Bouxsein, Lisa Langsetmo, Samaneh Farsijani, Deborah M Kado, Roberto Pacifici, Shivani Sahni, Douglas P Kiel
The gut microbiome affects the inflammatory environment through effects on T-cells, which influence the production of immune mediators and inflammatory cytokines that stimulate osteoclastogenesis and bone loss in mice. However, there are few large human studies of the gut microbiome and skeletal health. We investigated the association between the human gut microbiome and high resolution peripheral quantitative computed tomography (HR-pQCT) scans of the radius and tibia in two large cohorts; Framingham Heart Study (FHS [n=1227, age range: 32 - 89]), and the Osteoporosis in Men Study (MrOS [n=836, age range: 78 - 98])...
2023: Frontiers in Endocrinology
https://read.qxmd.com/read/37744229/inclusion-of-up-to-20-black-soldier-fly-larvae-meal-in-broiler-chicken-diet-has-a-minor-effect-on-caecal-microbiota
#29
JOURNAL ARTICLE
Jessica de Souza Vilela, Sarbast K Kheravii, Yadav Sharma Bajagai, Manisha Kolakshyapati, Terence Zimazile Sibanda, Shu-Biao Wu, Nigel R Andrew, Isabelle Ruhnke
BACKGROUND: The Black Soldier Fly larvae (BSFL) are a source of nutrients and bioactive compounds in broiler diets. Some components of the BSFL may serve as a prebiotic or may impact the intestinal microbiota of the broilers by other modes of action, which in turn can affect the health and performance of broilers. Here, we investigate the impact of up to 20% BSFL in broiler diets on the diversity and composition of the broiler's microbiota. METHODS: Four hundred broilers were fed five iso-nutritious experimental diets with increasing levels of BSFL meal reaching 0%, 5%, 10%, 15%, 20% in the finisher diets...
2023: PeerJ
https://read.qxmd.com/read/37721348/vasculitis-associated-with-adenosine-deaminase-2-deficiency-at-the-crossroads-between-beh%C3%A3-et-s-disease-and-autoinflammation-a-viewpoint
#30
JOURNAL ARTICLE
A Colangelo, F Tromby, G Cafaro, R Gerli, E Bartoloni, C Perricone
Adenosine deaminase 2 deficiency (DADA2) is a rare monogenic vasculopathy caused by loss-of-function homozygous or compound heterozygous mutations in ADA2, formerly CECR1 (cat eye syndrome chromosome region 1) gene. The DADA2 phenotype is widely heterogeneous, and patients may present with fever, weight loss, livedo reticularis/racemosa, digital ischemia, cutaneous ulceration, peripheral neuropathy, abdominal pain, bowel perforation, and portal or nephrogenic hypertension. More specific manifestations include early-onset ischemic or hemorrhagic stroke, mild immunodeficiency and hypogammaglobinemia, cytopenia, and vision disturbances...
September 18, 2023: Reumatismo
https://read.qxmd.com/read/37719263/deficiency-of-adenosine-deaminase-2-as-an-unrecognized-cause-of-early-onset-stroke-and-cranial-nerve-palsy
#31
JOURNAL ARTICLE
Elif Celikel, Fatma Aydin, Zahide Ekici Tekin, Tuba Kurt, Muge Sezer, Nilufer Tekgoz, Cuneyt Karagol, Serkan Coskun, Melike Mehves Kaplan, Aysegul Nese Citak Kurt, Banu Celikel Acar
OBJECTIVE: The aim of this study is to evaluate the clinical, laboratory, and radiological findings and prognosis of patients with adenosine deaminase 2 deficiency (DADA2) and to highlight the conditions that DADA2 should be considered in the differential diagnosis in patients with neurological findings. METHODS: A case series of six DADA2 patients was presented in this retrospective, descriptive study. Clinical and laboratory data, treatment protocols, and prognosis of the patients were recorded...
2023: Northern Clinics of Istanbul
https://read.qxmd.com/read/37713505/the-gut-microbiota-composition-is-linked-to-subsequent-occurrence-of-ventilator-associated-pneumonia-in-critically-ill-patients
#32
JOURNAL ARTICLE
Arthur Orieux, Raphaël Enaud, Sébastien Imbert, Philippe Boyer, Erwan Begot, Adrian Camino, Alexandre Boyer, Patrick Berger, Didier Gruson, Laurence Delhaes, Renaud Prevel
Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critically ill-ventilated patients. Oropharyngeal and lung microbiota have been demonstrated to be associated with VAP occurrence, but the involvement of gut microbiota has not been investigated so far. Therefore, the aim of this study is to compare the composition of the gut microbiota between patients who subsequently develop VAP and those who do not. A rectal swab was performed at admission of every consecutive patient into the intensive care unit (ICU) from October 2019 to March 2020...
September 15, 2023: Microbiology Spectrum
https://read.qxmd.com/read/37671197/impact-of-active-lifestyle-on-the-primary-school-children-saliva-microbiota-composition
#33
JOURNAL ARTICLE
Annamaria Mancini, Claudia Cerulli, Daniela Vitucci, Vito Alessandro Lasorsa, Daniela Parente, Andrea Di Credico, Stefania Orrù, Paolo Riccardo Brustio, Corrado Lupo, Alberto Rainoldi, Federico Schena, Mario Capasso, Pasqualina Buono
UNLABELLED: The aim of the study was to evaluate the effects of Active or Sedentary lifestyle on saliva microbiota composition in Italian schoolchildren. METHODS: Male (114) and female children (8-10 years) belonging to five primary schools in the neighborhoods of Turin were classified as active (A) or sedentary (S) based on PAQ-C-It questionnaire. PCR amplification of salivary DNA targeted the hypervariable V3-V4 regions of the 16S rRNA bacterial genes. DADA2 workflow was used to infer the Amplicon Sequence Variants and the taxonomic assignments; the beta-diversity was obtained by PCoA with the UniFrac method; LEfSe algorithm, threshold at 5%, and Log LDA cutoff at ±0...
2023: Frontiers in Nutrition
https://read.qxmd.com/read/37647436/a-new-cecr1-mutation-associated-with-severe-hematological-involvement-in-ada2-deficiency
#34
JOURNAL ARTICLE
Delia Nicoară, Cristina Niță, Ana Stanilă, Alexandru Martiniuc, Laura Popa, Eliana Petrescu, Mihaela Bătăneant, Ruxandra Ciofu, Adriana Guriță, Radu Tabăcaru, Ruxandra Ionescu, Laura Groșeanu
BACKGROUND: The deficiency of adenosine deaminase 2 (DADA2) is an autosomal recessively inherited disease resulting from loss-of-function mutations in ADA2, formerly named CECR1 (cat eye syndrome chromosome region, candidate 1) gene. Disease manifestations could be separated into three major phenotypes: inflammatory/vascular, immune dysregulatory, and hematologic; however, most patients presented with significant overlap between these three phenotype groups. CASE PRESENTATION: We present a case of DADA2 deficiency with disease onset at 3 years old, not recognized till the age of 18 with severe gastrointestinal vasculitis and recurrent episodes of neutropenia associated with a new CECR1 mutation...
August 2023: Immunity, Inflammation and Disease
https://read.qxmd.com/read/37646004/cerebral-aneurysms-and-recurrent-tias-in-a-42-year-old-patient-with-dada2-mutation-a-case-report
#35
JOURNAL ARTICLE
Netta Agajany, Liran Horev, Netanel Agajany, Gilad Kenan
OBJECTIVES: Deficiency of adenosine deaminase 2 (DADA2) is a rare, recessively inherited autoinflammatory disease with a wide clinical spectrum of manifestations, including strokes and vasculitis. METHODS: We report a case of a patient with DADA2 who presented with neurologic manifestations. RESULTS: A 42-year-old woman with a known diagnosis of polyarteritis nodosa experienced several episodes of TIAs. Neuroimaging revealed 2 aneurysms in unusual locations...
October 2023: Neurology. Genetics
https://read.qxmd.com/read/37633998/metagenomic-profiling-pipelines-improve-taxonomic-classification-for-16s-amplicon-sequencing-data
#36
JOURNAL ARTICLE
Aubrey R Odom, Tyler Faits, Eduardo Castro-Nallar, Keith A Crandall, W Evan Johnson
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon sequencing. However, the most-used bioinformatics tools cannot produce high quality genus-level or species-level taxonomic calls and may underestimate the potential accuracy of these calls. We used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, concentrating on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads...
August 26, 2023: Scientific Reports
https://read.qxmd.com/read/37609647/microbiome-dataset-of-bacterial-and-fungal-communities-in-anthosphere-of-twelve-different-wild-plants-in-south-korea
#37
JOURNAL ARTICLE
Jihoon Kim, Yingshun Cui, Haeun Lee, Seong-Jun Chun
This dataset provides detailed profiles of bacterial and fungal communities associated with flowers (anthosphere) of 12 different plant species collected from remote and secluded locations characterized by a flourishing and diverse plant ecosystem. In total, 144 flower samples were collected from 12 different wild plants. Bacterial 16S rRNA and fungal ITS genes obtained using the Illumina Miseq approach were used to describe the anthosphere. Metadata and raw sequences obtained in this study are available from the National Center for Biotechnology Information (BioProject ID: PRJNA983070)...
October 2023: Data in Brief
https://read.qxmd.com/read/37560524/an-independent-evaluation-in-a-crc-patient-cohort-of-microbiome-16s-rrna-sequence-analysis-methods-otu-clustering-dada2-and-deblur
#38
JOURNAL ARTICLE
Guang Liu, Tong Li, Xiaoyan Zhu, Xuanping Zhang, Jiayin Wang
16S rRNA is the universal gene of microbes, and it is often used as a target gene to obtain profiles of microbial communities via next-generation sequencing (NGS) technology. Traditionally, sequences are clustered into operational taxonomic units (OTUs) at a 97% threshold based on the taxonomic standard using 16S rRNA, and methods for the reduction of sequencing errors are bypassed, which may lead to false classification units. Several denoising algorithms have been published to solve this problem, such as DADA2 and Deblur, which can correct sequencing errors at single-nucleotide resolution by generating amplicon sequence variants (ASVs)...
2023: Frontiers in Microbiology
https://read.qxmd.com/read/37554448/intragenomic-diversity-of-the-v9-hypervariable-domain-in-eukaryotes-has-little-effect-on-metabarcoding
#39
JOURNAL ARTICLE
Olga Flegontova, Julius Lukeš, Aleš Horák
Metabarcoding revolutionized our understanding of diversity and ecology of microorganisms in different habitats. However, it is also associated with several inherent biases, one of which is associated with intragenomic diversity of a molecular barcode. Here, we compare intragenomic variability of the V9 region of the 18S rRNA gene in 19 eukaryotic phyla abundant in marine plankton. The level of intragenomic variability is comparable across all the phyla, and in most genomes and transcriptomes one V9 sequence and one OTU is predominant...
August 18, 2023: IScience
https://read.qxmd.com/read/37548813/a-narrative-review-of-the-neurological-manifestations-of-human-adenosine-deaminase-2-deficiency
#40
JOURNAL ARTICLE
Mariia Dzhus, Lisa Ehlers, Marjon Wouters, Katrien Jansen, Rik Schrijvers, Lien De Somer, Steven Vanderschueren, Marco Baggio, Leen Moens, Benjamin Verhaaren, Rik Lories, Giorgia Bucciol, Isabelle Meyts
Deficiency of human adenosine deaminase type 2 (DADA2) is a complex systemic autoinflammatory disorder characterized by vasculopathy, immune dysregulation, and hematologic abnormalities. The most notable neurological manifestations of DADA2 are strokes that can manifest with various neurological symptoms and are potentially fatal. However, neurological presentations can be diverse. We here present a review of the neurological manifestations of DADA2 to increase clinical awareness of DADA2 as the underlying diagnosis...
August 7, 2023: Journal of Clinical Immunology
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