MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways

Rusilowicz, Martin; Dickinson, Mike; Charlton, Adrian J.; O’Keefe, Simon; Wilson, Julie

doi:10.1371/journal.pone.0205968

Cited by 16 publications

(12 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The pathways in which the metabolites were significantly enriched, were processed in metabolites sets enrichment analysis (MSEA) and their significance was determined by p -values of the hypergeometric test. To study the change trend of the relative content of metabolites in different varieties, the average value of the relative content of different metabolites in each variety were standardized by z-score, and then k-means clustering analysis was performed [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

Metabolome Profiling of Eight Chinese Yam (Dioscorea polystachya Turcz.) Varieties Reveals Metabolite Diversity and Variety Specific Uses

Zeng

Liu

Huang

2021

Life

View full text Add to dashboard Cite

The Chinese yam (Dioscorea polystachya Turcz.) is an underutilized orphan tuber crop. However, in China it has been used in traditional medicine and food for centuries due to the presence of high starch, protein, fiber, and biologically active compounds. Knowledge on the metabolomic profiles of Chinese yam varieties is needed to explore the underutilized metabolites and variety specific uses. Here, the metabolome of eight Chinese yam varieties that are cultivated in different Chinese regions was profiled. A total of 431 metabolites belonging to different biochemical classes was detected. The majority of detected metabolites were classified as amino acids and derivatives. The different yam varieties offer unique uses; e.g., Hebei Ma Yam, Henan Huai Yam, and Henan Wild Yam were the most metabolically enriched and suitable as food and medicine. Yams from Hubei region had comparable nutritional profiles, which is most probably due to their geographical origin. Specifically, Henan Wild Yam had the highest concentrations of diosgenin, vitamins, and polysaccharides. Overall, this study presents a metabolome reference for D. polystachya varieties.

show abstract

Section: Methodsmentioning

confidence: 99%

Metabolome Profiling of Eight Chinese Yam (Dioscorea polystachya Turcz.) Varieties Reveals Metabolite Diversity and Variety Specific Uses

Zeng

Liu

Huang

2021

Life

View full text Add to dashboard Cite

show abstract

“…The mass range was set at 50–1200 m/z in a scan time of 0.3 s and an interscan delay of 0.02 s. System control and data collection were performed by MassLynx software (Waters Corporation, United States). The Progenesis QI software (v2.0) (Non-linear Dynamics, United Kingdom) was used for non-targeted signal detection, signal integration and feature alignment ( Rusilowicz, 2016 ). MetaScope embedded in the Progenesis QI was used to annotate metabolites not only based on neutral mass, isotope distribution and retention time, but also based on the collisional cross-sectional area and MS/MS fragmentation data in the HMDB database.…”

Section: Methodsmentioning

confidence: 99%

Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites

Zhong

Liu

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

More and more studies have indicated that gut microbiota takes part in the biosynthesis and metabolism of sex hormones. Inversely, sex hormones influence the composition of gut microbiota. However, whether microbiota in the gut and vagina is associated with estrus return of weaning sows is largely unknown. Here, using 16S rRNA gene sequencing in 158 fecal and 50 vaginal samples, we reported the shifts in the gut and vaginal microbiota between normal return and non-return sows. In fecal samples, Lactobacillus and S24-7 were enriched in normal return sows, while Streptococcus luteciae, Lachnospiraceae, Clostridium, and Mogibacterium had higher abundance in non-return sows. In vaginal swabs, the operational taxonomic units (OTUs) annotated to Clostridiales, Ruminoccaceae, and Oscillospira were enriched in normal return sows, while those OTUs annotated to Campylobacter, Anaerococcus, Parvimonas, Finegoldia, and Dorea had higher abundances in non-return sows. Co-abundance group (CAG) analysis repeated the identification of the bacterial taxa associated with the estrus return of weaning sows. The predicted functional capacities in both gut and vaginal microbiome were changed between normal return and non-return sows. Serum metabolome profiles were determined by non-targeted metabolome analysis in seven normal return and six non-return sows. The metabolite features having higher abundance in normal return sows were enriched in the pathways Steroid hormone biosynthesis, Starch and sucrose metabolism, Galactose metabolism, and Vitamin B6 metabolism, while the metabolite features belonging to organic acids and derivatives, indoles and derivatives, sulfoxides, and lignans and neolignans had significantly higher abundance in non-return sows. Correlation analysis found that the changes in gut microbiota were associated with the shifts of serum metabolites and suggested that certain bacteria might affect estrus return of weaning sow through serum metabolites. These findings may provide new insights for understanding the role of the gut and vaginal microbiota in sow return to estrus after weaning.

show abstract

“…Raw data from UPLC–QTOFMS underwent peak selection and grouping, retention time correction, second peak grouping, and isotope and adducts annotation using Progenesis QI (Rusilowicz, 2016). Each retained peak was then normalized to the QC sample using MetNormalize (Shen et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows

et al. 2019

View full text Add to dashboard Cite

Perinatal care is important in mammals due to its contribution to fetal growth, maternal health, and lactation. Substantial changes in host hormones, metabolism, and immunity around the parturition period may be accompanied by alterations in the gut microbiome. However, to our knowledge, changes in the gut microbiome and their contribution to the shifts in host metabolism around parturition have not been investigated in pigs. Furthermore, pigs are an ideal biomedical model for studying the interactions of the gut microbiota with host metabolism, due to the ease of controlling feeding conditions. Here we report dramatic remodeling of the gut microbiota and the potential functional capacity during the late stages of pregnancy (5 days before parturition, LP) to postpartum (within 6 h after delivery, PO) in both experimental and validated populations of sows (n = 107). The richness of bacteria in the gut of both pregnant and delivery sows significantly decreased, whilst the β-diversity dramatically expanded. The ratio of Bacteroidetes to Firmicutes, and the relative abundance of Prevotella significantly decreased, whilst the relative abundance of the predominant genus Lactobacillus significantly increased from LP to PO state. The predicted functional capacities of the gut microbiome related to amino acid metabolism, the metabolism of cofactors and vitamins, and glycan biosynthesis were significantly decreased from LP to PO state. However, the abundance of the functional capacities associated with carbohydrate and lipid metabolism were increased. Consistent with these changes, serum metabolites enriched at the LP stage were associated with the metabolism of amino acids and vitamins. In contrast, metabolites enriched at the PO stage were related to lipid metabolism. We further identified that the richness and β-diversity of the gut microbiota and the abundance of Lactobacillus accounted for shifts in the levels of bile acid metabolites associated with lipid metabolism. The results suggest that host-microbiota interactions during the perinatal period impact host metabolism. These benefit the lactation of sows by providing energy from lipid metabolism for milk production.

show abstract

MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways

Cited by 16 publications

References 47 publications

Metabolome Profiling of Eight Chinese Yam (Dioscorea polystachya Turcz.) Varieties Reveals Metabolite Diversity and Variety Specific Uses

Metabolome Profiling of Eight Chinese Yam (Dioscorea polystachya Turcz.) Varieties Reveals Metabolite Diversity and Variety Specific Uses

Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites

Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows

Contact Info

Product

Resources

About