scholarly journals Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242553
Author(s):  
Fernanda Sayuri do Nascimento ◽  
Milena Oliveira Suzuki ◽  
João Victor Taba ◽  
Vitoria Carneiro de Mattos ◽  
Leonardo Zumerkorn Pipek ◽  
...  
Keyword(s):  
Sequence Data ◽  
Control Group ◽  
Case Group ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Sequencing Data ◽  
16S Sequencing ◽  
Disease Biomarkers ◽  
Link Type ◽  
Bile Samples

Background The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Methods Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes. Results The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases. Trial registration NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426.

scholarly journals Analysis of Biliary Microbiota in Hepatobiliopancreatic Diseases Compared to Healthy People [MICROBILIO]: Study Protocol

2020 ◽  
Author(s):  
Fernanda Sayuri do Nascimento ◽  
Milena Oliveira Suzuki ◽  
João Victor Taba ◽  
Vitoria Carneiro de Mattos ◽  
Leonardo Zumerkorn Pipek ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Principal Component ◽  
Control Group ◽  
Case Group ◽  
Disease Biomarkers ◽  
Student’S T ◽  
New Treatments ◽  
Bile Samples ◽  
Student’S T Test

Abstract Background: The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.Methods: Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). From the DNA extracted from the samples, the microbiomes will be sequenced by 16S ribosomal RNA (rRNA) pyrosequencing methods. Student’s t-test will be performed with SPSS version 20 for Windows and the Mann-Whitney test will be performed using R software and Python scripts. A principal component analysis signals will be developed as discriminative analysis.Results: The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.Conclusions: We believe that the investigation of the biliary tract microbiota will provide benefits such as early diagnosis and new treatments. This should improve quality of life and survival, specially in malignant diseases. Thus, this research will give expectations to further investigation in the biliary microbiota.Trial registration: NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

scholarly journals Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

2021 ◽  
Author(s):  
Marvin A. Altamia ◽  
J. Reuben Shipway ◽  
David Stein ◽  
Meghan A. Betcher ◽  
Jennifer M. Fung ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Data ◽  
Amino Acid Identity ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08T, Bs12T and Bsc2T, are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter . The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12T, purple; others beige to brown), marine salt requirement (Bs12T, Bsc2T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08T and T. turnerae strains) and the ability to respire nitrate (Bs08T). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08T=ATCC TSD-121T=KCTC 62964T), Teredinibacter purpureus sp. nov. (type strain Bs12T=ATCC TSD-122T=KCTC 62965T) and Teredinibacter franksiae sp. nov. (type strain Bsc2T=ATCC TSD-123T=KCTC 62966T).

scholarly journals Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota

2020 ◽  
Vol 9 (5) ◽  
pp. 1589
Author(s):  
Kyung Eun Yun ◽  
Jimin Kim ◽  
Mi-hyun Kim ◽  
Eunkyo Park ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Large Scale ◽  
Blood Lipids ◽  
Density Lipoprotein ◽  
Lipoprotein Cholesterol ◽  
Control Group ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Lipid Markers

The gut microbiota has been linked to blood lipids. However, the relationship between the gut microbiome and other lipid markers like apolipoproteins A1 (apoA1) and B (apoB) as well as classical lipid markers in Asians remain unclear. Here, we examined the associations between gut microbial diversity and taxonomic compositions with both apolipoproteins and lipid markers in a large number of Korean patients. The fecal 16S rRNA gene sequencing data from 1141 subjects were analyzed and subjects were categorized into control group (G0) or abnormal group (G1) according to blood lipid measurements. The microbial diversity and several taxa of the gut microbiota were significantly associated with triglyceride, apoA1, and apoB levels, but not with total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol levels. The alpha diversity of the gut microbiota was inversely associated with high triglyceride level. Interestingly, G1 of apoA1 showed increased microbial richness and distinct microbial community compared with G0 of apoA1. A high abundance of Fusobacteria and low abundance of Oscillospira were found in the hypertriglyceridemia group. In this large-scale study, we identified associations of gut microbiota with apolipoproteins and classical lipid markers, indicating that the gut microbiota may be an important target for regulating blood lipids.

scholarly journals Systematic processing of ribosomal RNA gene amplicon sequencing data

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Julien Tremblay ◽  
Etienne Yergeau
Keyword(s):  
Ribosomal Rna ◽  
High Performance ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Low Cost ◽  
Marker Gene ◽  
Fine Tuning ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Data Types

Abstract Background With the advent of high-throughput sequencing, microbiology is becoming increasingly data-intensive. Because of its low cost, robust databases, and established bioinformatic workflows, sequencing of 16S/18S/ITS ribosomal RNA (rRNA) gene amplicons, which provides a marker of choice for phylogenetic studies, has become ubiquitous. Many established end-to-end bioinformatic pipelines are available to perform short amplicon sequence data analysis. These pipelines suit a general audience, but few options exist for more specialized users who are experienced in code scripting, Linux-based systems, and high-performance computing (HPC) environments. For such an audience, existing pipelines can be limiting to fully leverage modern HPC capabilities and perform tweaking and optimization operations. Moreover, a wealth of stand-alone software packages that perform specific targeted bioinformatic tasks are increasingly accessible, and finding a way to easily integrate these applications in a pipeline is critical to the evolution of bioinformatic methodologies. Results Here we describe AmpliconTagger, a short rRNA marker gene amplicon pipeline coded in a Python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. It is designed to work within an HPC environment, supporting a complex network of job dependencies with a smart-restart mechanism in case of job failure or parameter modifications. As proof of concept, we present end results obtained with AmpliconTagger using 16S, 18S, ITS rRNA short gene amplicons and Pacific Biosciences long-read amplicon data types as input. Conclusions Using a selection of published algorithms for generating operational taxonomic units and amplicon sequence variants and for computing downstream taxonomic summaries and diversity metrics, we demonstrate the performance and versatility of our pipeline for systematic analyses of amplicon sequence data.

scholarly journals 16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Saidu Abdullahi ◽  
Hazzeman Haris ◽  
Kamarul Z. Zarkasi ◽  
Hamzah G. Amir
Keyword(s):  
Heavy Metal ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Mimosa Pudica ◽  
Sequencing Data ◽  
Content Type ◽  
Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

scholarly journals Enteractinococcus coprophilus gen. nov., sp. nov., of the family Micrococcaceae , isolated from Panthera tigris amoyensis faeces, and transfer of Yaniella fodinae Dhanjal et al. 2011 to the genus Enteractinococcus as Enteractinococcus fodinae comb. nov.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2710-2716 ◽  
Author(s):  
Yan-Ru Cao ◽  
Yi Jiang ◽  
Rong-Xian Jin ◽  
Li Han ◽  
Wen-Xiang He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
New Genus ◽  
Sequence Data ◽  
Rrna Gene ◽  
Panthera Tigris ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Phosphatidylinositol Mannosides

A novel actinobacterium, designated strain YIM 100590T, was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590T is a member of the family Micrococcaceae . Cells were coccoid to oval (0.7–1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10–37 °C (optimum 28 °C) and at pH 7.0–11.0 (optimum pH 8.0). The major fatty acids were iso-C15 : 0 (32.22 %), anteiso-C15 : 0 (31.64 %) and iso-C16 : 0 (17.38 %). The peptidoglycan was of A4α type (l-Lys–Gly–l-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9 %) and MK-8 (8.3 %). The DNA G+C content of strain YIM 100590T was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae . On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590T is considered to represent a novel species of a new genus within the family Micrococcaceae , for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590T ( = DSM 24083T = JCM 17352T). Yaniella fodinae DSM 22966T was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5T = DSM 22966T = JCM 17931T = MTCC 9846T).

scholarly journals Massilia norwichensis sp. nov., isolated from an air sample

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 56-64 ◽  
Author(s):  
Ivana Orthová ◽  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
René Kaden ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9T, isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9T identified Massilia haematophila CCUG 38318T, M. niastensis 5516S-1T (both 97.7 % similarity), M. aerilata 5516S-11T (97.4 %) and M. tieshanensis TS3T (97.4 %) as the next closest relatives. In partial gyrB and lepA sequences, NS9T shared the highest similarities with M. haematophila CCUG 38318T (94.5 %) and M. aerilata 5516-11T (94.3 %), respectively. These sequence data demonstrate the affiliation of NS9T to the genus Massilia . The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9T to the genus Massilia . Major fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C10 : 0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA–DNA hybridizations demonstrate that strain NS9T is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9T ( = CCUG 65457T = LMG 28164T).

scholarly journals Iron Bacterial Phylogeny and their Execution Towards Iron Availability in Equatorial Indian Ocean and Coastal Arabian Sea

2013 ◽  
Vol 62 (4) ◽  
pp. 391-400 ◽  
Author(s):  
RAJU RAJASABAPATHY ◽  
CHELLANDI MOHANDASS ◽  
AJAKKALAMOOLE SRINIVAS VIJAYARAJ ◽  
VARSHA VINAYAK MADIVAL ◽  
RAM MURTI MEENA
Keyword(s):  
Indian Ocean ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Arabian Sea ◽  
Sequence Data ◽  
Restriction Analysis ◽  
Equatorial Indian Ocean ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Bacterial Strains

Based on distinct colony morphology, color, size, shape and certain other traits, 92 bacterial isolates were investigated to understand their managerial ability on iron from the Arabian Sea and Equatorial Indian Ocean samples. The ARDRA (amplified rDNA restriction analysis) applied to eliminate the duplication of the bacterial strains, resulted 39 different banding patterns. The 16S rRNA gene sequencing data indicate the dominancy of three phylogenetic groups, alpha-Proteobacteria (10.25%), gamma-Proteobacteria (35.89%) and Bacilli (53.84%) in these waters. Marinobacter and Bacillus were the only common genera from both of the regions. Pseudoalteromonas, Halomonas, Rheinheimera, Staphylococcus and Idiomarina were some of the other genera obtained from the Arabian Sea. Erythrobacter, Roseovarius, Sagittula and Nitratireductor were found mostly in Equatorial Indian Ocean. In addition, 16S rRNA gene sequence data of some of our iron bacterial strains belong to novel species and one isolate ASS2A could form a new genus. Close to 23% of the isolates were able to produce high affinity sets of ligands like siderophores to mediate iron transport into the cell. The current study indicated that the Equatorial Indian Ocean species were well adapted to oxidize iron as an electron acceptor and the Arabian Sea species preferably go through siderophore production.

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