Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women

Menni, Cristina; Zierer, Jonas; Pallister, Tess; Jackson, Matthew A.; Long, Tao; Mohney, Robert P.; Steves, Claire J.; Spector, Tim D.; Valdes, Ana M.

doi:10.1038/s41598-017-10382-2

Cited by 189 publications

(136 citation statements)

References 80 publications

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“…While higher SCFA levels in the stool with fibre‐free EN compared to PN have been reported (Sobotka et al , ; Schneider et al , ), the reason for this is unclear. The EN formula provided also contained omega 3 fatty acids, which have recently been associated with increased abundance of butyrate‐producing bacteria in healthy individuals (Watson et al , ), which may be independent of dietary fibre intake (Menni et al , ). Further investigation of the benefit of fibre and omega‐3 fatty acid‐containing EN on clinical outcomes in HPCT is warranted.…”

Section: Discussionmentioning

confidence: 99%

Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post‐allogeneic transplantation

Andersen¹,

Staudacher

Weber³

et al. 2019

Br J Haematol

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Summary Nutrition support is frequently required post‐allogeneic haematopoietic progenitor cell transplantation (HPCT); however, the impact of mode of feeding on the gastrointestinal microbiome has not been explored. This study aimed to determine if there is a difference in the microbiome between patients receiving enteral nutrition (EN) and parenteral nutrition (PN) post‐allogeneic HPCT. Twenty‐three patients received either early EN or PN when required. Stool samples were collected at 30 days post‐transplant and analysed with shotgun metagenomic sequencing. There was no difference in microbial diversity between patients who received predominantly EN (n = 13) vs. PN (n = 10) however patients who received predominantly EN had greater abundance of Faecalibacterium (P < 0·001) and ruminococcus E bromii (P = 0·026). Patients who had minimal oral intake for a longer duration during provision of nutrition support had a different overall microbial profile (P = 0·044), lower microbial diversity (P = 0·004) and lower abundance of faecalibacterium prausnitzii_C (P = 0·030) and Blautia (P = 0·007) compared to patients with greater oral intake. Lower microbial diversity was found in patients who received additional beta lactam antibiotics (P = 0·042) or had a longer length of hospital stay (P = 0·019). Post‐HPCT oral intake should be encouraged to maintain microbiota diversity and, if nutrition support is required, EN may promote a more optimal microbiota profile.

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Section: Discussionmentioning

confidence: 99%

Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post‐allogeneic transplantation

Andersen¹,

Staudacher

Weber³

et al. 2019

Br J Haematol

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“…70 In another larger, cross-sectional study with 876 women, Menni et al demonstrated that polyunsaturated fats were associated with an increase in microbial diversity and an increase in members of the Lachnospiraceae family. 71 …”

Section: Environmental Factorsmentioning

confidence: 99%

Influence of Early Life, Diet, and the Environment on the Microbiome

Dong

Gupta

2019

Clinical Gastroenterology and Hepatology

148

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Advances in sequencing technology and bioinformatics have greatly enhanced our ability to understand the human microbiome. Over the last decade, a growing body of literature has linked nutrition and the environment to the microbiome and is now thought to be an important contributor to overall health. This paper reviews the literature from the past 10 years to highlight the influence of environmental factors such as diet, early life adversity and stress in shaping and modifying our microbiome towards health and disease. The review shows that many factors such as the mode of delivery, breast milk, stress, diet and medications can greatly influence the development of our gut microbiome and potentially make us more prone to certain diseases. By incorporating environmental factors into models that study the microbiome in the setting of health and disease, may provide a better understanding of disease and potentially new areas of treatment. To highlight this, we will additionally explore the role of the environment and the microbiome in the development of obesity and functional bowel disorders.

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“…a gold standard profile. Alpha diversity metrics summarize the variety (or richness) and distribution of taxa present in a profile [29] and, among other uses, is commonly used to observe global shifts in community structure as a result of some environmental parameter [30][31][32][33]. The simplest alpha diversity metric is the number of taxa present in a given environment.…”

Section: Alpha Diversity Metricsmentioning

confidence: 99%

Assessing taxonomic metagenome profilers with OPAL

Meyer¹,

Bremges²,

Belmann

et al. 2018

Preprint

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Taxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples of DNA isolated directly from a microbial community. Over the past years, there has been an explosive growth of software and algorithms for this task, resulting in a need for more systematic comparisons of these methods based on relevant performance criteria. Here, we present OPAL, a software package implementing commonly used performance metrics, including those of the first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, OPAL implements diversity metrics from microbial ecology, as well as run time and memory efficiency measurements. By allowing users to customize the relative importance of metrics, OPAL facilitates in-depth performance comparisons, as well as the development of new methods and data analysis workflows. To demonstrate the application, we compared seven profilers on benchmark datasets of the first and second CAMI challenges using all metrics and performance measurements available in OPAL. The software is implemented in Python 3 and available under the Apache 2.0 license on GitHub (https://github.com/CAMI-challenge/OPAL). Author summaryThere are many computational approaches for inferring the presence and relative abundance of taxa (i.e. taxonomic profiling) from shotgun metagenome samples of microbial communities, making systematic performance evaluations a very important task. However, there has yet to be introduced a computational framework in which profiler performances can be compared. This delays method development and applied studies, as researchers need to implement their own custom evaluation frameworks. Here, we present OPAL, a software package that facilitates standardized comparisons of taxonomic metagenome profilers. It implements a variety of performance metrics July 19, 2018 1/15 frequently employed in microbiome research, including runtime and memory usage, and generates comparison reports and visualizations. OPAL thus facilitates and accelerates benchmarking of taxonomic profiling techniques on ground truth data. This enables researchers to arrive at informed decisions about which computational techniques to use for specific datasets and research questions.

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Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women

Cited by 189 publications

References 80 publications

Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post‐allogeneic transplantation

Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post‐allogeneic transplantation

Influence of Early Life, Diet, and the Environment on the Microbiome

Assessing taxonomic metagenome profilers with OPAL

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