scholarly journals Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

2016 ◽  
Vol 50 (11) ◽  
pp. 6079-6090 ◽  
Author(s):  
Laura Treu ◽  
Stefano Campanaro ◽  
Panagiotis G. Kougias ◽  
Xinyu Zhu ◽  
Irini Angelidaki
Keyword(s):  
Fatty Acid ◽  
Microbial Community ◽  
Species Level ◽  
Community Members ◽  
Transcriptional Responses ◽  
Acid Addition

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Omega-3 fatty acid addition during pregnancy

2018 ◽  
Author(s):  
Philippa Middleton ◽  
Judith C Gomersall ◽  
Jacqueline F Gould ◽  
Emily Shepherd ◽  
Sjurdur F Olsen ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Omega 3 ◽  
Omega 3 Fatty Acid ◽  
Acid Addition

ATGL-mediated triglyceride turnover and the regulation of mitochondrial capacity in skeletal muscle

2015 ◽  
Vol 308 (11) ◽  
pp. E960-E970 ◽  
Author(s):  
Ruth C. R. Meex ◽  
Andrew J. Hoy ◽  
Rachael M. Mason ◽  
Sheree D. Martin ◽  
Sean L. McGee ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Fatty Acid ◽  
Lipid Droplets ◽  
Target Genes ◽  
Control Point ◽  
Hormone Sensitive Lipase ◽  
Acid Oxidation ◽  
Minor Importance ◽  
Transcriptional Responses ◽  
Mitochondrial Capacity

Emerging evidence indicates that skeletal muscle lipid droplets are an important control point for intracellular lipid homeostasis and that regulating fatty acid fluxes from lipid droplets might influence mitochondrial capacity. We used pharmacological blockers of the major triglyceride lipases, adipose triglyceride lipase (ATGL) and hormone-sensitive lipase, to show that a large proportion of the fatty acids that are transported into myotubes are trafficked through the intramyocellular triglyceride pool. We next tested whether increasing lipolysis from intramyocellular lipid droplets could activate transcriptional responses to enhance mitochondrial and fatty acid oxidative capacity. ATGL was overexpressed by adenoviral and adenoassociated viral infection in C2C12 myotubes and the tibialis anterior muscle of C57Bl/6 mice, respectively. ATGL overexpression in C2C12 myotubes increased lipolysis, which was associated with increased peroxisome proliferator-activated receptor (PPAR)-∂ activity, transcriptional upregulation of some PPAR∂ target genes, and enhanced mitochondrial capacity. The transcriptional responses were specific to ATGL actions and not a generalized increase in fatty acid flux in the myotubes. Marked ATGL overexpression (20-fold) induced modest molecular changes in the skeletal muscle of mice, but these effects were not sufficient to alter fatty acid oxidation. Together, these data demonstrate the importance of lipid droplets for myocellular fatty acid trafficking and the capacity to modulate mitochondrial capacity by enhancing lipid droplet lipolysis in vitro; however, this adaptive program is of minor importance when superimposing the normal metabolic stresses encountered in free-moving animals.

scholarly journals Fatty acid is a potential agent for bone tissue induction: In vitro and in vivo approach

2017 ◽  
Vol 242 (18) ◽  
pp. 1765-1771 ◽  
Author(s):  
Guinea BC Cardoso ◽  
Erivelto Chacon ◽  
Priscila GL Chacon ◽  
Pedro Bordeaux-Rego ◽  
Adriana SS Duarte ◽  
...  
Keyword(s):  
Stem Cells ◽  
Oleic Acid ◽  
Fatty Acid ◽  
Bone Tissue ◽  
In Vivo Studies ◽  
Surrounding Tissue ◽  
Bone Induction ◽  
Acid Addition

Our hypothesis was to investigate the fatty acid potential as a bone induction factor. In vitro and in vivo studies were performed to evaluate this approach. Oleic acid was used in a 0.5 wt.% concentration. Polycaprolactone was used as the polymeric matrix by combining solvent-casting and particulate-leaching techniques, with a final porosity of 70 wt.%, investigated by SEM images. Contact angle measurements were produced to investigate the influence of oleic acid on polycaprolactone chains. Cell culture was performed using adipocyte-derived stem cells to evaluate biocompatibility and bioactivity properties. In addition, in vivo studies were performed to evaluate the induction potential of oleic acid addition. Adipocyte-derived stem cells were used to provide differentiation after 21 days of culture. Likewise, information were obtained with in vivo data and cellular invagination was observed on both scaffolds (polycaprolactone and polycaprolactone /oleic acid); interestingly, the scaffold with oleic acid addition demonstrated that cellular migrations are not related to the surrounding tissue, indicating bioactive potential. Our hypothesis is that fatty acid may be used as a potential induction factor for bone tissue engineering. The study’s findings indicate oleic acid as a possible agent for bone induction, according to data on cell differentiation, proliferation, and migration. Impact statement The biomaterial combined in this study on bone regeneration is innovative and shows promising results in the treatment of bone lesions. Polycaprolactone (PCL) and oleic acid have been studied separately. In this research, we combined biomaterials to assess the stimulus and the speed of bone healing.

scholarly journals DISCo-microbe: design of an identifiable synthetic community of microbes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8534 ◽  
Author(s):  
Dana L. Carper ◽  
Travis J. Lawrence ◽  
Alyssa A. Carrell ◽  
Dale A. Pelletier ◽  
David J. Weston
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Dna Sequence ◽  
Sequence Alignment ◽  
Amplicon Sequencing ◽  
Ribosomal Database Project ◽  
Community Members ◽  
Dna Sequence Alignment ◽  
Diverse Community

Background Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. Results To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. Conclusions DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).

scholarly journals Effects of Dietary Fiber on Cecal Short Chain Fatty Acid and Microbial Community of Broiler and Layer Chicks

2015 ◽  
Author(s):  
John C. F. Hsieh ◽  
Muhammed Walugembe ◽  
Nick J. Koszewski ◽  
Susan J. Lamont ◽  
Max F. Rothschild
Keyword(s):  
Fatty Acid ◽  
Microbial Community ◽  
Dietary Fiber ◽  
Short Chain Fatty Acid ◽  
Chain Fatty Acid ◽  
Short Chain

scholarly journals Crowdsourcing snake identification with online communities of professional herpetologists and avocational snake enthusiasts

2021 ◽  
Vol 8 (1) ◽  
pp. 201273
Author(s):  
A. M. Durso ◽  
I. Bolon ◽  
A. R. Kleinhesselink ◽  
M. R. Mondardini ◽  
J. L. Fernandez-Marquez ◽  
...  
Keyword(s):  
Citizen Science ◽  
Gold Standard ◽  
Healthcare Workers ◽  
Geographical Origin ◽  
Species Level ◽  
Community Members ◽  
Venomous Snake ◽  
Building Capacity ◽  
The World ◽  
Treatment Data

Species identification can be challenging for biologists, healthcare practitioners and members of the general public. Snakes are no exception, and the potential medical consequences of venomous snake misidentification can be significant. Here, we collected data on identification of 100 snake species by building a week-long online citizen science challenge which attracted more than 1000 participants from around the world. We show that a large community including both professional herpetologists and skilled avocational snake enthusiasts with the potential to quickly (less than 2 min) and accurately (69–90%; see text) identify snakes is active online around the clock, but that only a small fraction of community members are proficient at identifying snakes to the species level, even when provided with the snake's geographical origin. Nevertheless, participants showed great enthusiasm and engagement, and our study provides evidence that innovative citizen science/crowdsourcing approaches can play significant roles in training and building capacity. Although identification by an expert familiar with the local snake fauna will always be the gold standard, we suggest that healthcare workers, clinicians, epidemiologists and other parties interested in snakebite could become more connected to these communities, and that professional herpetologists and skilled avocational snake enthusiasts could organize ways to help connect medical professionals to crowdsourcing platforms. Involving skilled avocational snake enthusiasts in decision making could build the capacity of healthcare workers to identify snakes more quickly, specifically and accurately, and ultimately improve snakebite treatment data and outcomes.

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