Microbial Communities, Structure, and Function

2012 ◽  
Keyword(s):  
Microbial Communities ◽  
Structure And Function ◽  
And Function

Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields

2013 ◽  
Vol 15 (9) ◽  
pp. 2588-2602 ◽  
Author(s):  
Ana Fernandez Scavino ◽  
Yang Ji ◽  
Judith Pump ◽  
Melanie Klose ◽  
Peter Claus ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Structure And Function ◽  
Rice Fields ◽  
Irrigated Rice ◽  
And Function

scholarly journals Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data

2020 ◽  
Vol 36 (11) ◽  
pp. 3365-3371
Author(s):  
Yaxin Xue ◽  
Anders Lanzén ◽  
Inge Jonassen
Keyword(s):  
Microbial Communities ◽  
Real World ◽  
Structure And Function ◽  
Rrna Genes ◽  
Supplementary Information ◽  
Metagenomic Data ◽  
Total Rna ◽  
Transcriptomic Data ◽  
And Function ◽  
Complex Datasets

Abstract Motivation Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all three domains of life simultaneously. A major step of this approach is the reconstruction of full-length taxonomic marker genes such as the small subunit ribosomal RNA. However, current tools for this purpose are mainly targeted towards analysis of amplicon and metagenomic data and thus lack the ability to handle the massive and complex datasets typically resulting from total RNA experiments. Results In this work, we introduce MetaRib, a new tool for reconstructing ribosomal gene sequences from total RNA meta-transcriptomic data. MetaRib is based on the popular rRNA assembly program EMIRGE, together with several improvements. We address the challenge posed by large complex datasets by integrating sub-assembly, dereplication and mapping in an iterative approach, with additional post-processing steps. We applied the method to both simulated and real-world datasets. Our results show that MetaRib can deal with larger datasets and recover more rRNA genes, which achieve around 60 times speedup and higher F1 score compared to EMIRGE in simulated datasets. In the real-world dataset, it shows similar trends but recovers more contigs compared with a previous analysis based on random sub-sampling, while enabling the comparison of individual contig abundances across samples for the first time. Availability and implementation The source code of MetaRib is freely available at https://github.com/yxxue/MetaRib. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Structure and function of alpine and arctic soil microbial communities

2005 ◽  
Vol 156 (7) ◽  
pp. 775-784 ◽  
Author(s):  
Diana R. Nemergut ◽  
Elizabeth K. Costello ◽  
Allen F. Meyer ◽  
Monte Y. Pescador ◽  
Michael N. Weintraub ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Structure And Function ◽  
Soil Microbial ◽  
Arctic Soil ◽  
And Function

scholarly journals Structure and function of the bacterial and fungal gut flora of Neotropical butterflies

2017 ◽  
Author(s):  
Alison Ravenscraft ◽  
Michelle Berry ◽  
Tobin Hammer ◽  
Kabir Peay ◽  
Carol Boggs
Keyword(s):  
Amino Acids ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Microbial Community Composition ◽  
Structure And Function ◽  
Feeding Guilds ◽  
Gut Flora ◽  
Microbial Composition ◽  
Host Diet ◽  
And Function

AbstractThe relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut flora compare to food microbial communities? Finally, are gut flora functionally adapted to the chemical makeup of host foods? To answer these questions we captured nearly 300 Costa Rican butterflies representing over 50 species, six families and two feeding guilds: frugivores and nectivores. We characterized the bacteria and fungi in guts, wild fruits and wild nectars via amplicon sequencing and assessed the catabolic abilities of the gut flora via culture-based assays.Gut communities were distinct from food communities, suggesting that the gut environment acts as a strong filter on potential colonists. Nevertheless, gut flora varied widely among individuals and species. On average, a pair of butterflies shared 21% of their bacterial species and 6% of their fungi. Host species explained 25-30% of total variation in microbial communities while host diet explained 4%. However, diet was still relevant at the individual microbe level—half of the most abundant microbial species differed in abundance between frugivores and nectivores. Diet was also related to the functional profile of gut flora: compared to frugivores, nectivores’ gut flora exhibited increased catabolism of sugars and sugar alcohols and decreased catabolism of amino acids, carboxylic acids and dicarboxylic acids. Since fermented juice contains more amino acids and less sugar than nectar, it appears that host diet filters the gut flora by favoring microbes that digest compounds abundant in foods.By quantifying the degree to which gut communities vary among host individuals, species and dietary guilds and evaluating how gut microbial composition and catabolic potential are related to host diet, this study deepens our understanding of the structure and function of one of the most complex and ubiquitous symbioses in the animal kingdom.

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