keyword
https://read.qxmd.com/read/38535312/integrating-genome-sequencing-and-untargeted-metabolomics-in-monozygotic-twins-with-a-rare-complex-neurological-disorder
#1
Rulan Shaath, Aljazi Al-Maraghi, Haytham Ali, Jehan AlRayahi, Adam D Kennedy, Karen L DeBalsi, Sura Hussein, Najwa Elbashir, Sujitha S Padmajeya, Sasirekha Palaniswamy, Sarah H Elsea, Ammira A Akil, Noha A Yousri, Khalid A Fakhro
Multi-omics approaches, which integrate genomics, transcriptomics, proteomics, and metabolomics, have emerged as powerful tools in the diagnosis of rare diseases. We used untargeted metabolomics and whole-genome sequencing (WGS) to gain a more comprehensive understanding of a rare disease with a complex presentation affecting female twins from a consanguineous family. The sisters presented with polymicrogyria, a Dandy-Walker malformation, respiratory distress, and multiorgan dysfunctions. Through WGS, we identified two rare homozygous variants in both subjects, a pathogenic variant in ADGRG1 (p...
March 4, 2024: Metabolites
https://read.qxmd.com/read/38532461/placental-tlr-recognition-of-salivary-and-subgingival-microbiota-is-associated-with-pregnancy-complications
#2
JOURNAL ARTICLE
Kazune Pax, Nurcan Buduneli, Murat Alan, Pinar Meric, Onder Gurlek, Shareef M Dabdoub, Purnima S Kumar
BACKGROUND: Pre-term birth, the leading cause of neonatal mortality, has been associated with maternal periodontal disease and the presence of oral pathogens in the placenta. However, the mechanisms that underpin this link are not known. This investigation aimed to identify the origins of placental microbiota and to interrogate the association between parturition complications and immune recognition of placental microbial motifs. Video Abstract METHODS: Saliva, plaque, serum, and placenta were collected during 130 full-term (FT), pre-term (PT), or pre-term complicated by pre-eclampsia (PTPE) deliveries and subjected to whole-genome shotgun sequencing...
March 26, 2024: Microbiome
https://read.qxmd.com/read/38528457/full-length-16s-rrna-gene-sequencing-by-pacbio-improves-taxonomic-resolution-in-human-microbiome-samples
#3
JOURNAL ARTICLE
Elena Buetas, Marta Jordán-López, Andrés López-Roldán, Giuseppe D'Auria, Llucia Martínez-Priego, Griselda De Marco, Miguel Carda-Diéguez, Alex Mira
BACKGROUND: Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution...
March 25, 2024: BMC Genomics
https://read.qxmd.com/read/38522229/exposure-to-environmental-toxicants-is-associated-with-gut-microbiome-dysbiosis-insulin-resistance-and-obesity
#4
JOURNAL ARTICLE
Partho Sen, Yong Fan, Jennifer J Schlezinger, Stanislav D Ehrlich, Thomas F Webster, Tuulia Hyötyläinen, Oluf Pedersen, Matej Orešič
Environmental toxicants (ETs) are associated with adverse health outcomes. Here we hypothesized that exposures to ETs are linked with obesity and insulin resistance partly through a dysbiotic gut microbiota and changes in the serum levels of secondary bile acids (BAs). Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 men and 143 women, aged 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m2 ) using a combination of targeted and suspect screening approaches...
March 20, 2024: Environment International
https://read.qxmd.com/read/38515176/cataloging-the-phylogenetic-diversity-of-human-bladder-bacterial-isolates
#5
JOURNAL ARTICLE
Jingjie Du, Mark Khemmani, Thomas Halverson, Adriana Ene, Roberto Limeira, Lana Tinawi, Baylie R Hochstedler-Kramer, Melline Fontes Noronha, Catherine Putonti, Alan J Wolfe
BACKGROUND: Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS: To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females...
March 21, 2024: Genome Biology
https://read.qxmd.com/read/38514648/integrative-metagenomic-and-metabolomic-analyses-reveal-the-potential-of-gut-microbiota-to-exacerbate-acute-pancreatitis
#6
JOURNAL ARTICLE
Jianjun Liu, Qiulong Yan, Shenghui Li, Juying Jiao, Yiming Hao, Guixin Zhang, Qingkai Zhang, Fei Luo, Yue Zhang, Qingbo Lv, Wenzhe Zhang, Aiqin Zhang, Huiyi Song, Yi Xin, Yufang Ma, Lawrence Owusu, Xiaochi Ma, Peiyuan Yin, Dong Shang
Early dysbiosis in the gut microbiota may contribute to the severity of acute pancreatitis (AP), however, a comprehensive understanding of the gut microbiome, potential pathobionts, and host metabolome in individuals with AP remains elusive. Hence, we employed fecal whole-metagenome shotgun sequencing in 82 AP patients and 115 matched healthy controls, complemented by untargeted serum metabolome and lipidome profiling in a subset of participants. Analyses of the gut microbiome in AP patients revealed reduced diversity, disrupted microbial functions, and altered abundance of 77 species, influenced by both etiology and severity...
March 21, 2024: NPJ Biofilms and Microbiomes
https://read.qxmd.com/read/38504332/contigs-directed-gene-annotation-condiga-for-accurate-protein-sequence-database-construction-in-metaproteomics
#7
JOURNAL ARTICLE
Enhui Wu, Vijini Mallawaarachchi, Jinzhi Zhao, Yi Yang, Hebin Liu, Xiaoqing Wang, Chengpin Shen, Yu Lin, Liang Qiao
BACKGROUND: Microbiota are closely associated with human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. It is generally recommended to use metagenomic data from the same samples to construct the protein sequence database for metaproteomic data analysis...
March 19, 2024: Microbiome
https://read.qxmd.com/read/38500040/comprehensive-genomic-analysis-of-bacillus-subtilis-and-bacillus-paralicheniformis-associated-with-the-pearl-millet-panicle-reveals-their-antimicrobial-potential-against-important-plant-pathogens
#8
JOURNAL ARTICLE
Mushineni Ashajyothi, Shivannegowda Mahadevakumar, Y N Venkatesh, Pullabhotla V S R N Sarma, Chalasani Danteswari, Alexander Balamurugan, Ganesan Prakash, Vikas Khandelwal, C Tarasatyavathi, Appa Rao Podile, Mysore S Kirankumar, Siddaiah Chandranayaka
BACKGROUND: Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36 found to have beneficial traits including plant growth promotion and broad-spectrum antifungal activity towards taxonomically diverse plant pathogens. Understanding the genomes will assist in devising a bioformulation for crop protection while exploiting their beneficial functional roles...
March 18, 2024: BMC Plant Biology
https://read.qxmd.com/read/38491814/understanding-gut-microbiome-based-machine-learning-platforms-a-review-on-therapeutic-approaches-using-deep-learning
#9
REVIEW
Shilpa Malakar, Priya Sutaoney, Harishkumar Madhyastha, Kamal Shah, Nagendra Singh Chauhan, Paromita Banerjee
Human beings possess trillions of microbial cells in a symbiotic relationship. This relationship benefits both partners for a long time. The gut microbiota helps in many bodily functions from harvesting energy from digested food to strengthening biochemical barriers of the gut and intestine. But the changes in microbiota composition and bacteria that can enter the gastrointestinal tract can cause infection. Several approaches like culture-independent techniques such as high-throughput and meta-omics projects targeting 16S ribosomal RNA (rRNA) sequencing are popular methods to investigate the composition of the human gastrointestinal tract microbiota and taxonomically characterizing microbial communities...
March 2024: Chemical Biology & Drug Design
https://read.qxmd.com/read/38488368/eight-complete-genome-sequences-of-bacteria-isolated-from-laboratory-stock-of-giant-kelp-gametophytes
#10
JOURNAL ARTICLE
Bernadeth Tolentino, Sergey Nuzhdin
We report whole-genome sequences of eight bacteria isolated from laboratory-kept Macrocystis pyrifera gametophytes. The bacterial culture collection is maintained in cryostorage and will be utilized in future applications as inoculants. The genomes were assembled using Oxford Nanopore Technology long-read sequencing.
March 15, 2024: Microbiology Resource Announcements
https://read.qxmd.com/read/38488359/comparison-of-metagenomic-and-traditional-methods-for-diagnosis-of-e-coli-enteric-infections
#11
JOURNAL ARTICLE
C Royer, N V Patin, K J Jesser, A Peña-Gonzalez, J K Hatt, G Trueba, K Levy, K T Konstantinidis
UNLABELLED: Diarrheagenic Escherichia coli , collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients...
March 15, 2024: MBio
https://read.qxmd.com/read/38480804/whole-body-metabolic-modelling-reveals-microbiome-and-genomic-interactions-on-reduced-urine-formate-levels-in-alzheimer-s-disease
#12
JOURNAL ARTICLE
Filippo Martinelli, Almut Heinken, Ann-Kristin Henning, Maria A Ulmer, Tim Hensen, Antonio González, Matthias Arnold, Sanjay Asthana, Kathrin Budde, Corinne D Engelman, Mehrbod Estaki, Hans-Jörgen Grabe, Margo B Heston, Sterling Johnson, Gabi Kastenmüller, Cameron Martino, Daniel McDonald, Federico E Rey, Ingo Kilimann, Olive Peters, Xiao Wang, Eike Jakob Spruth, Anja Schneider, Klaus Fliessbach, Jens Wiltfang, Niels Hansen, Wenzel Glanz, Katharina Buerger, Daniel Janowitz, Christoph Laske, Matthias H Munk, Annika Spottke, Nina Roy, Matthias Nauck, Stefan Teipel, Rob Knight, Rima F Kaddurah-Daouk, Barbara B Bendlin, Johannes Hertel, Ines Thiele
In this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models...
March 13, 2024: Scientific Reports
https://read.qxmd.com/read/38461372/alterations-of-lacrimal-sac-microbiota-in-failed-dacryocystorhinostomy-the-lacriome-paper-6
#13
JOURNAL ARTICLE
Mohammad Javed Ali
PURPOSE: To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR). METHODS: A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the IlluminaTM platform following DNA extraction and library preparation...
March 9, 2024: Seminars in Ophthalmology
https://read.qxmd.com/read/38453815/comparative-whole-genome-analysis-of-face-derived-streptococcus-infantis-cx-4-unravels-the-functions-related-to-skin-barrier
#14
JOURNAL ARTICLE
Haeun Lee, Dong-Geol Lee, HyungWoo Jo, Young Mok Heo, Chaeyun Baek, Hye-Been Kim, Geunhwa Park, Seunghyun Kang, Wooseok Lee, Seyoung Mun, Kyudong Han
BACKGROUND: The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S...
March 7, 2024: Genes & Genomics
https://read.qxmd.com/read/38443809/characterization-of-rumen-microbiome-and-immune-genes-expression-of-crossbred-beef-steers-with-divergent-residual-feed-intake-phenotypes
#15
JOURNAL ARTICLE
Godstime Taiwo, Olanrewaju B Morenikeji, Modoluwamu Idowu, Taylor Sidney, Ajiboye Adekunle, Andres Pech Cervantes, Sunday Peters, Ibukun M Ogunade
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30...
March 5, 2024: BMC Genomics
https://read.qxmd.com/read/38420205/metagenomic-profiling-of-viral-and-microbial-communities-from-the-pox-lesions-of-lumpy-skin-disease-virus-and-sheeppox-virus-infected-hosts
#16
JOURNAL ARTICLE
Fedor S Sharko, Ali Mazloum, Alena O Krotova, Olga P Byadovskaya, Larisa B Prokhvatilova, Ilya A Chvala, Ustin E Zolotikov, Alexandra D Kozlova, Anastasia S Krylova, Erika V Grosfeld, Anastasia V Prokopenko, Aleksei A Korzhenkov, Maxim V Patrushev, Zorigto B Namsaraev, Alexander V Sprygin, Stepan V Toshchakov
INTRODUCTION: It has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis...
2024: Frontiers in Veterinary Science
https://read.qxmd.com/read/38399723/butyric-acid-supplementation-reduces-changes-in-the-taxonomic-and-functional-composition-of-gut-microbiota-caused-by-h-pylori-eradication-therapy
#17
JOURNAL ARTICLE
Sayar Abdulkhakov, Maria Markelova, Dilyara Safina, Maria Siniagina, Dilyara Khusnutdinova, Rustam Abdulkhakov, Tatiana Grigoryeva
UNLABELLED: H. pylori eradication therapy leads to significant changes in the gut microbiome, including influence on the gut microbiome's functional potential. Probiotics are one of the most studied potential methods for reducing the microbiota-related consequences of antibiotics. However, the beneficial effects of probiotics are still under discussion. In addition, there are some concerns about the safety of probiotics, emphasizing the need for research of other therapeutic interventions...
February 3, 2024: Microorganisms
https://read.qxmd.com/read/38399691/unique-changes-in-the-lung-microbiome-following-the-development-of-chronic-lung-allograft-dysfunction
#18
JOURNAL ARTICLE
Yeuni Yu, Yun Hak Kim, Woo Hyun Cho, Dohyung Kim, Min Wook So, Bong Soo Son, Hye Ju Yeo
The importance of lung microbiome changes in developing chronic lung allograft dysfunction (CLAD) after lung transplantation is poorly understood. The lung microbiome-immune interaction may be critical in developing CLAD. In this context, examining alterations in the microbiome and immune cells of the lungs following CLAD, in comparison to the lung condition immediately after transplantation, can offer valuable insights. Four adult patients who underwent lung retransplantation between January 2019 and June 2020 were included in this study...
January 29, 2024: Microorganisms
https://read.qxmd.com/read/38374282/insights-into-gut-microbiomes-in-stem-cell-transplantation-by-comprehensive-shotgun-long-read-sequencing
#19
JOURNAL ARTICLE
Philipp Spohr, Sebastian Scharf, Anna Rommerskirchen, Birgit Henrich, Paul Jäger, Gunnar W Klau, Rainer Haas, Alexander Dilthey, Klaus Pfeffer
The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics...
February 19, 2024: Scientific Reports
https://read.qxmd.com/read/38366679/neopolyploidy-has-variable-effects-on-the-diversity-and-composition-of-the-wild-strawberry-microbiome
#20
JOURNAL ARTICLE
Thomas J Anneberg, Nevin P Cullen, Elizabeth M O'Neill, Na Wei, Tia-Lynn Ashman
PREMISE: Whole-genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities...
February 17, 2024: American Journal of Botany
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