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381.
Fernando Puente-Sánchez Matthias Hoetzinger Moritz Buck Stefan Bertilsson 《Molecular ecology resources》2023,23(7):1724-1736
At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined “species”, whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution. 相似文献
382.
Akihiko Suzuki Koyuki Akuzawa Kazunobu Kogi Keiichi Ueda Miwa Suzuki 《Marine Mammal Science》2021,37(1):207-219
Captive environments impact the microbiota of captive animals; however, the comparison of microbiota between wild and captive dolphins has been poorly investigated. To explore the impact of a captive environment, we characterized the fecal microbiota of nine wild and four captive Indo-Pacific bottlenose dolphins, Tursiops aduncus, using a next-generation sequencing and revealed differences in the fecal microbiota between the analyzed groups. Statistical differences in abundances of the phyla Firmicutes and Proteobacteria were found between the wild and captive dolphins. Thirty-six genera (22.9% of the total genera detected in all dolphins) were shared between the groups, whereas 79 (50.3%) and 42 (26.8%) genera were found only in the wild or captive dolphins, respectively. Several pathogenic bacterial genera, including Morganella and Mycoplasma, were detected only in the captive dolphins, and the genus Lactobacillus was found only in the wild dolphins. LefSe and SIMPER analyses revealed that the genus Clostridium sensu stricto 1 was significantly more abundant in the captive dolphins than in the wild ones and contributed the most to the dissimilarity of fecal microbiota between the groups. Our results indicate that the captive environment impacts the fecal microbiota of dolphins and reinforces the importance of monitoring potentially pathogenic bacteria in captivity. 相似文献
383.
Cindy H. Nakatsu Ravi Barabote Sue Thompson David Bruce Chris Detter Thomas Brettin Cliff Han Federico Beasley Weimin Chen Allan Konopka Gary Xie 《Standards in genomic sciences》2013,8(1):106-111
This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo. 相似文献
384.
《Current biology : CB》2022,32(23):5209-5218.e5
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《Cell host & microbe》2020,27(4):585-600.e4
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Luis Martínez Villegas Paulo Filemon Paolucci Pimenta 《Memórias do Instituto Oswaldo Cruz》2014,109(5):672-684
Anophelines harbour a diverse microbial consortium that may represent an extended
gene pool for the host. The proposed effects of the insect microbiota span
physiological, metabolic and immune processes. Here we synthesise how current
metagenomic tools combined with classical culture-dependent techniques provide new
insights in the elucidation of the role of the Anopheles-associated
microbiota. Many proposed malaria control strategies have been based upon the
immunomodulating effects that the bacterial components of the microbiota appear to
exert and their ability to express anti-Plasmodium peptides. The
number of identified bacterial taxa has increased in the current “omics” era and the
available data are mostly scattered or in “tables” that are difficult to exploit.
Published microbiota reports for multiple anopheline species were compiled in an
Excel® spreadsheet. We then filtered the microbiota data using a
continent-oriented criterion and generated a visual correlation showing the exclusive
and shared bacterial genera among four continents. The data suggested the existence
of a core group of bacteria associated in a stable manner with their anopheline
hosts. However, the lack of data from Neotropical vectors may reduce the possibility
of defining the core microbiota and understanding the mosquito-bacteria interactive
consortium. 相似文献
390.
Miguel I. Uyaguari-Diaz Jared R. Slobodan Matthew J. Nesbitt Matthew A. Croxen Judith Isaac-Renton Natalie A. Prystajecky Patrick Tang 《Journal of visualized experiments : JoVE》2015,(98)
Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads. 相似文献