scholarly journals Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora Glomerata (Chlorophyta)

2016 ◽  
Author(s):  
Michael J. Braus ◽  
Linda E. Graham ◽  
Thea L. Whitman
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Open Water ◽  
Spatial And Temporal Variation ◽  
Cladophora Glomerata ◽  
Growth Season ◽  
Organic C ◽  
Lake Mendota ◽  
Bacterial Microbiota ◽  
Sequencing Studies

ABSTRACTThe branched periphytic green alga Cladophora glomerata, often abundant in nearshore waters of lakes and rivers worldwide, plays important ecosystem roles, some mediated by epibiotic microbiota that benefit from host-provided surface, organic C, and O2. Previous microscopy and high throughput sequencing studies have indicated surprising epibiont taxonomic and functional diversity, but have not included adequate consideration of sample replication or the potential for spatial and temporal variation. Here we report the results of 16S rRNA amplicon-based phylum-to-genus taxonomic analysis of Cladophora-associated bacterial epibiota sampled in replicate from three microsites and at six times during the open-water season of 2014, from the same lake locale (Picnic Point, Lake Mendota, Dane Co., WI, USA) explored by high throughput sequencing studies in two previous years. Statistical methods were used to test null hypotheses that the bacterial community: 1) is homogeneous across microsites tested, and 2) does not change over the course of a growth season or among successive years. Results indicated a dynamic microbial community that is more strongly influenced by sampling day during the growth season than by microsite variation. A surprising diversity of bacterial genera known to be associated with the key function of methane-oxidation (methanotrophy)-including relatively high-abundance of Crenothrix, Methylomonas, and Methylocaldum–showed intra-seasonal and inter-annual variability possibly related to temperature differences, and microsite preferences possibly related to variation in methane abundance. By contrast, a core assemblage of bacterial genera seems to persist over a growth season and from year-to-year, possibly transmitted by a persistent attached host resting stage.

scholarly journals Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

2020 ◽  
Author(s):  
Emily N. Junkins ◽  
Bradley S. Stevenson
Keyword(s):  
High Throughput ◽  
Drug Targets ◽  
High Throughput Sequencing ◽  
Multidrug Resistant ◽  
Molecular Techniques ◽  
Bioactive Metabolites ◽  
Plate Count ◽  
Molecular Tools ◽  
Vast Number ◽  
Sequencing Studies

AbstractMolecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.ImportanceCultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.

scholarly journals Beyond the Ribosome: Extra-translational Functions of tRNA Fragments

2016 ◽  
Vol 11s1 ◽  
pp. BMI.S35904 ◽  
Author(s):  
Kevin W. Diebel ◽  
Kun Zhou ◽  
Aaron B. Clarke ◽  
Lynne T. Bemis
Keyword(s):  
Data Analysis ◽  
High Throughput ◽  
Biological Samples ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Degradation Products ◽  
Noncoding Rnas ◽  
Transfer Rnas ◽  
Sequencing Studies ◽  
Domains Of Life

High-throughput sequencing studies of small RNAs reveal a complex milieu of noncoding RNAs in biological samples. Early data analysis was often limited to microRNAs due to their regulatory nature and potential as biomarkers; however, many more classes of noncoding RNAs are now being recognized. A class of fragments initially excluded from analysis were those derived from transfer RNAs (tRNAs) because they were thought to be degradation products. More recently, critical cellular function has been attributed to tRNA fragments (tRFs), and their conservation across all domains of life has propelled them into an emerging area of scientific study. The biogenesis of tRFs is currently being elucidated, and initial studies show that a diverse array of tRFs are genera ted from all parts of a tRNA molecule. The goal of this review was to present what is currently known about tRFs and their potential as biomarkers for the earlier detection of disease.

scholarly journals Fulcrum: condensing redundant reads from high-throughput sequencing studies

2012 ◽  
Vol 28 (10) ◽  
pp. 1324-1327 ◽  
Author(s):  
Matthew S. Burriesci ◽  
Erik M. Lehnert ◽  
John R. Pringle
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Studies

scholarly journals Using familial information for variant filtering in high-throughput sequencing studies

2014 ◽  
Vol 133 (11) ◽  
pp. 1331-1341 ◽  
Author(s):  
Melanie Bahlo ◽  
Rick Tankard ◽  
Vesna Lukic ◽  
Karen L. Oliver ◽  
Katherine R. Smith
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Variant Filtering ◽  
Sequencing Studies

scholarly journals Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding

2020 ◽  
Author(s):  
Simon P. Kelow ◽  
Jared Adolf-Bryfogle ◽  
Roland L. Dunbrack
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Data Bank ◽  
Antigen Binding ◽  
Sequence Variability ◽  
Antigen Binding Site ◽  
Sequencing Studies ◽  
Variable Domains ◽  
Complementarity Determining Regions ◽  
Hiv 1

AbstractAntibody variable domains contain “complementarity determining regions” (CDRs), the loops that form the antigen binding site. CDRs1-3 are recognized as the canonical CDRs. However, a fourth loop sits adjacent to CDR1 and CDR2 and joins the D and E strands on the antibody v-type fold. This “DE loop” is usually treated as a framework region, even though mutations in the loop affect the conformation of the CDRs and residues in the DE loop occasionally contact antigen. We analyzed the length, structure, and sequence features of all DE loops in the Protein Data Bank, as well as millions of sequences from HIV-1 infected and naïve patients. We refer to the DE loop as H4 and L4 in the heavy and light chain respectively. Clustering the backbone conformations of the most common length of L4 (6 residues) reveals four conformations: two κ-only clusters, one λ-only cluster, and one mixed κ/λ cluster. The vast majority of H4 loops are length-8 and exist primarily in one conformation; a secondary conformation represents a small fraction of H4-8 structures. H4 sequence variability exceeds that of the antibody framework in naïve human high-throughput sequences, and both L4 and H4 sequence variability from λ and heavy germline sequences exceed that of germline framework regions. Finally, we identified dozens of structures in the PDB with insertions in the DE loop, all related to broadly neutralizing HIV-1 antibodies, as well as antibody sequences from high-throughput sequencing studies of HIV-infected individuals, illuminating a possible role in humoral immunity to HIV-1.

A roadmap for high‐throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture

2019 ◽  
Vol 19 (3) ◽  
pp. 609-622 ◽  
Author(s):  
Lauren C. White ◽  
Claudia Fontsere ◽  
Esther Lizano ◽  
David A. Hughes ◽  
Samuel Angedakin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Wild Animal ◽  
Hybridization Capture ◽  
Animal Populations ◽  
Sequencing Studies ◽  
Noninvasive Samples

scholarly journals Exploring the Individual Bacterial Microbiota of Questing Ixodes ricinus Nymphs

2021 ◽  
Vol 9 (7) ◽  
pp. 1526
Author(s):  
Aurélien Alafaci ◽  
Alexandre Crépin ◽  
Sabine Beaubert ◽  
Jean-Marc Berjeaud ◽  
Vincent Delafont ◽  
...  
Keyword(s):  
Ixodes Ricinus ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Animal Health ◽  
Abundant Species ◽  
Hard Tick ◽  
16S Gene ◽  
Bacterial Microbiota ◽  
Co Detection ◽  
The Individual

Ixodes ricinus is the most common hard tick species in Europe and an important vector of pathogens of human and animal health concerns. The rise of high-throughput sequencing has facilitated the identification of many tick-borne pathogens and, more globally, of various microbiota members depending on the scale of concern. In this study, we aimed to assess the bacterial diversity of individual I. ricinus questing nymphs collected in France using high-throughput 16S gene metabarcoding. From 180 dragging-collected nymphs, we identified more than 700 bacterial genera, of which about 20 are abundantly represented (>1% of total reads). Together with 136 other genera assigned, they constitute a core internal microbiota in this study. We also identified 20 individuals carrying Borreliella. The most abundant species is B. afzelii, known to be one of the bacteria responsible for Lyme disease in Europe. Co-detection of up to four Borreliella genospecies within the same individual has also been retrieved. The detection and co-detection rate of Borreliella in I. ricinus nymphs is high and raises the question of interactions between these bacteria and the communities constituting the internal microbiota.

scholarly journals Comparison of three clustering approaches for detecting novel environmental microbial diversity

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1692 ◽  
Author(s):  
Dominik Forster ◽  
Micah Dunthorn ◽  
Thorsten Stoeck ◽  
Frédéric Mahé
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Sequence Similarity ◽  
Pairwise Alignment ◽  
Clustering Methods ◽  
Sequencing Studies ◽  
Similarity Networks ◽  
Sequence Similarity Networks

Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR2) database using threede novoapproaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR2. Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.

Sign in / Sign up

Export Citation Format

Share Document