Benefits of merging paired-end reads before pre-processing environmental metagenomics data

2022 ◽  
Vol 61 ◽  
pp. 100914
Author(s):  
Midhuna Immaculate Joseph Maran ◽  
Dicky John Davis G.
Keyword(s):  
Metagenomics Data

scholarly journals Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽  
2021 ◽  
Vol 6 (5) ◽  
pp. 44
Author(s):  
Jae-Hyun Lim ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Sampling Site ◽  
Community Change ◽  
Rrna Gene ◽  
Water Column Stratification ◽  
Metagenomics Data ◽  
Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

scholarly journals Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics

2021 ◽  
Author(s):  
Leyuan Li ◽  
Zhibin Ning ◽  
Xu Zhang ◽  
James Butcher ◽  
Caitlin Simopoulos ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Protein Level ◽  
Functional Organization ◽  
Human Microbiome ◽  
Functional Redundancy ◽  
Human Gut ◽  
Functional Roles ◽  
Human Gut Microbiome ◽  
Metagenomics Data ◽  
Network Approaches

Functional redundancy is a key property of ecosystems and represents the fact that phylogenetically unrelated taxa can play similar functional roles within an ecosystem. The redundancy of potential functions of human microbiome has been recently quantified using metagenomics data. Yet, the redundancy of functions which are actually expressed within the human microbiome remains largely unexplored. Here, we quantify the protein-level functional redundancy in the human gut microbiome using metaproteomics and network approaches. In particular, our ultra-deep metaproteomics approach revealed high protein-level functional redundancy and high nestedness in proteomic content networks - bipartite graphs that connect taxa with their expressed functions. We further examined multiple metaproteomics datasets and showed that various environmental factors, including individuality, biogeography, xenobiotics, and disease, significantly altered the protein-level functional redundancy. Finally, by projecting the bipartite proteomic content networks into unipartite weighted genus networks, functional hub genera across individual microbiomes were discovered, suggesting that there may be a universal principle of functional organization in microbiome assembly.

Analysis of Metagenomics Data

2011 ◽  
pp. 219-229 ◽  
Author(s):  
Elizabeth M. Glass ◽  
Folker Meyer
Keyword(s):  
Metagenomics Data

scholarly journals Bambara groundnut soil metagenomics data

Data in Brief ◽  
2020 ◽  
Vol 30 ◽  
pp. 105542
Author(s):  
Caroline Fadeke Ajilogba ◽  
Olubukola Oluranti Babalola
Keyword(s):  
Bambara Groundnut ◽  
Metagenomics Data ◽  
Soil Metagenomics

scholarly journals PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data

2020 ◽  
Vol 36 (10) ◽  
pp. 3043-3048 ◽  
Author(s):  
Michael A Peabody ◽  
Wing Yin Venus Lau ◽  
Gemma R Hoad ◽  
Baofeng Jia ◽  
Finlay Maguire ◽  
...  
Keyword(s):  
Water Quality ◽  
Subcellular Localization ◽  
Microbial Communities ◽  
Cell Envelope ◽  
Supplementary Information ◽  
Protein Subcellular Localization ◽  
Metagenomic Sequence ◽  
Archaeal Protein ◽  
Wide Range ◽  
Metagenomics Data

Abstract Motivation Many methods for microbial protein subcellular localization (SCL) prediction exist; however, none is readily available for analysis of metagenomic sequence data, despite growing interest from researchers studying microbial communities in humans, agri-food relevant organisms and in other environments (e.g. for identification of cell-surface biomarkers for rapid protein-based diagnostic tests). We wished to also identify new markers of water quality from freshwater samples collected from pristine versus pollution-impacted watersheds. Results We report PSORTm, the first bioinformatics tool designed for prediction of diverse bacterial and archaeal protein SCL from metagenomics data. PSORTm incorporates components of PSORTb, one of the most precise and widely used protein SCL predictors, with an automated classification by cell envelope. An evaluation using 5-fold cross-validation with in silico-fragmented sequences with known localization showed that PSORTm maintains PSORTb’s high precision, while sensitivity increases proportionately with metagenomic sequence fragment length. PSORTm’s read-based analysis was similar to PSORTb-based analysis of metagenome-assembled genomes (MAGs); however, the latter requires non-trivial manual classification of each MAG by cell envelope, and cannot make use of unassembled sequences. Analysis of the watershed samples revealed the importance of normalization and identified potential biomarkers of water quality. This method should be useful for examining a wide range of microbial communities, including human microbiomes, and other microbiomes of medical, environmental or industrial importance. Availability and implementation Documentation, source code and docker containers are available for running PSORTm locally at https://www.psort.org/psortm/ (freely available, open-source software under GNU General Public License Version 3). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics

2019 ◽  
Vol 20 (S23) ◽  
Author(s):  
Chen Li ◽  
Yiqi Jiang ◽  
Shuaicheng Li
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Structure ◽  
Real Data ◽  
Time Profile ◽  
Structural Variations ◽  
Structure Variation ◽  
Local Strains ◽  
Number Of Microorganisms ◽  
Metagenomics Data

Abstract Background Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs. Results In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable. Conclusions Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.

scholarly journals Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Emilie E. L. Muller
Keyword(s):  
Microbial Community ◽  
Global Change ◽  
Niche Breadth ◽  
Microbial Populations ◽  
Ecosystem Stability ◽  
Great Opportunity ◽  
Metagenomics Data ◽  
Integrated Omics ◽  
Current Context

ABSTRACT Integrated omics applied to microbial communities offers a great opportunity to analyze the niche breadths (i.e., resource and condition ranges usable by a species) of constituent populations, ranging from generalists, with a broad niche breadth, to specialists, with a narrow one. In this context, extracellular metabolomics measurements describe resource spaces available to microbial populations; dedicated analyses of metagenomics data serve to describe the fundamental niches of constituent populations, and functional meta-omics becomes a proxy to characterize the realized niches of populations and their variations though time or space. Thus, the combination of environmental omics and its thorough interpretation allows us to directly describe niche breadths of constituent populations of a microbial community, precisely and in situ. This will greatly facilitate studies of the causes influencing ecosystem stability, resistance, and resilience, as well as generation of the necessary knowledge to model and predict the fate of any ecosystem in the current context of global change.

scholarly journals Metagenomic Sequences of Three Drinking Water and Two Shower Hose Biofilm Samples Treated with or without Copper-Silver Ionization

2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Anke Stüken ◽  
Thomas H. A. Haverkamp
Keyword(s):  
Drinking Water ◽  
Microbial Communities ◽  
Tap Water ◽  
Data Sets ◽  
Sequence Analyses ◽  
Illumina Hiseq ◽  
Shotgun Metagenomics ◽  
Premise Plumbing ◽  
Plumbing Systems ◽  
Metagenomics Data

We announce five shotgun metagenomics data sets from two Norwegian premise plumbing systems. The samples were shotgun sequenced on two lanes of an Illumina HiSeq 3000 instrument (THRUplex chemistry, 151 bp, paired-end reads), providing an extensive resource for sequence analyses of tap water and biofilm microbial communities.

scholarly journals Genome Sequence ofCoxiella-Like Endosymbiont Strain CLE-RmD, a Bacterial Agent in the Cattle Tick (Rhipicephalus microplus) Deutsch Strain

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Arunachalam Ramaiah ◽  
Gregory A. Dasch
Keyword(s):  
Genome Sequence ◽  
Rhipicephalus Microplus ◽  
Cattle Tick ◽  
Partial Genome Sequence ◽  
Content Type ◽  
Bacterial Agent ◽  
Southern Cattle Tick ◽  
Metagenomics Data ◽  
Partial Genome

ABSTRACTWe report a partial genome sequence for theCoxiella-like endosymbiont strain CLE-RmD, assembled from metagenomics data obtained from the southern cattle tick (Rhipicephalus microplus) Deutsch strain.

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