Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas

Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.

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Consuming Different Structural Parts of Bamboo Induce Gut Microbiome Changes in Captive Giant Pandas

Current Microbiology ◽

10.1007/s00284-021-02503-y ◽

2021 ◽

Author(s):

Zheng Yan ◽

Qin Xu ◽

Walter H. Hsu ◽

Stephan Schmitz Esser ◽

James Ayala ◽

...

Keyword(s):

Gut Microbiome ◽

Tricarboxylic Acid Cycle ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Giant Pandas ◽

Bamboo Shoots ◽

Different Seasons ◽

Structural Parts ◽

And Function

AbstractGiant pandas consume different structural parts of bamboo (shoots, leaves and culms) during different seasons. Previous research showed different bamboo parts have varying nutritional content and that a long-term diet consisting of a single part of bamboo resulted in remarkable metabolic changes within captive giant pandas. However, the effects on the gut microbiome of giant pandas, as a result of a single bamboo part diet, have not been investigated. Here, we evaluated the changes in gut microbial communities based on single bamboo part diets and their potential implications by using 16S rRNA gene-based amplicon sequencing and metagenome shotgun sequencing. We found that the composition and function of the gut microbiome from captive giant pandas fed exclusively culms were significantly different from that of individuals fed shoots or leaves. During the culm feeding period, the gut microbiome showed strongest digestive capabilities for cellulose, hemicellulose and starch, and had the highest potential abilities for the biosynthesis of bile acids, fatty acids and amino acids. This suggests the microbiome aids in breaking down culm, which is more difficult for giant pandas to digest, as a means to compensate for the nutrient poor content of the culm. Genes related to fatty acid metabolism and tricarboxylic acid cycle enzymes were more abundant during the leaf stage diet than that in the shoot and culm stages. Thus, the microbiome may help giant pandas, which typically have low lipase levels, with fat digestion. These results illustrate that adaptive changes in the gut microbiome community and function may be an important mechanism to aid giant panda digestion when consuming different structural parts of bamboo.

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The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

Scientific Reports ◽

10.1038/s41598-021-95146-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Pierre Legendre ◽

Claude Guertin

Keyword(s):

Microbial Community ◽

Gut Microbiome ◽

Strong Predictor ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Food Sources ◽

Microbiome Composition ◽

Living Organisms ◽

Insect Gut ◽

Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

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Dysbiosis of Gut Microbiota with Increased Trimethylamine N-oxide Level in Patients with Large Artery Atherosclerotic and Cardioembolic Strokes

10.21203/rs.3.rs-20073/v1 ◽

2020 ◽

Author(s):

Dong-Juan Xu ◽

Kai Cheng Wang ◽

Lin-Bo Yuan ◽

Qiong-Qiong Lin ◽

Hong-Fei Li ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Control Group ◽

Large Artery ◽

Microbiome Composition ◽

Plaque Area ◽

Liquid Chromatography Tandem Mass ◽

And Function ◽

Dietary Choline ◽

Asymptomatic Control

Abstract Background — With the establishment of the concept of the gut–brain axis, increasing evidence has shown that the gut microbiome plays an important role in the pathogenesis of cardiovascular diseases. Gut bacteria can transform dietary choline, L-carnitine, and trimethylamine N -oxide (TMAO) into trimethylamine, which can be oxidized into TMAO again in the liver and participate in atherogenesis. However, only few studies have described alterations in the gut microbiota composition and function in cardioembolic (CE) and large artery atherosclerotic (LAA) strokes. Methods and Results — A case–control study was performed on patients with LAA and CE strokes. TMAO was determined via liquid chromatography tandem mass spectrometry. Gut microbiome was profiled through Illumina sequencing of the 16S ribosomal RNA gene (V4–V5 regions). The TMAO levels in the plasma of patients with LAA and CE strokes were significantly increased (TMAO: LAA stroke, 2931±456.4 ng/mL vs. CE stroke, 4220±577.6 ng/mL vs. control, 1663±117.8 ng/mL; P < 0.05). The TMAO level in patients with LAA stroke was positively correlated with the carotid plaque area (rho = 0.333, 95% confidence interval = 0.08 to 0.55, and P = 0.0093). The composition and function of gut microbiomes in the LAA and CE stroke groups were significantly different from those of the asymptomatic control. In addition to the significantly increased α and β diversities, the gut microbiome composition and function showed that the LAA group had more microorganisms than the asymptomatic control group; such microorganisms convert dietary source choline, TMAO to TMA. Parabacteroides and Streptococcus exhibited the strongest association with LAA and CE strokes. Conclusions — This study established the compositional and functional alterations of gut microbiomes in patients with LAA and CE strokes and the relationship between plasma TMAO and gut microbiota. The findings suggest the potential of using gut microbiota as a biomarker for patients with LAA and CE strokes.

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Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial

Diabetes Care ◽

10.2337/dc20-2257 ◽

2021 ◽

pp. dc202257

Author(s):

Noel T. Mueller ◽

Moira K. Differding ◽

Mingyu Zhang ◽

Nisa M. Maruthur ◽

Stephen P. Juraschek ◽

...

Keyword(s):

Fatty Acids ◽

Randomized Trial ◽

Gut Microbiome ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Microbiome Composition ◽

And Function ◽

Chain Fatty Acids

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Dietary sphinganine is selectively assimilated by members of the gut microbiome

10.1101/2020.06.08.140665 ◽

2020 ◽

Author(s):

Min-Ting Lee ◽

Henry H. Le ◽

Elizabeth L. Johnson

Keyword(s):

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Dietary Lipids ◽

Rrna Gene ◽

Bioactive Components ◽

Microbiome Composition ◽

Metabolic Products ◽

Comparative Metabolomics ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

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Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease

Children ◽

10.3390/children5120160 ◽

2018 ◽

Vol 5 (12) ◽

pp. 160 ◽

Cited By ~ 11

Author(s):

Anica I. Mohammadkhah ◽

Eoin B. Simpson ◽

Stephanie G. Patterson ◽

Jane F. Ferguson

Keyword(s):

Metabolic Disease ◽

Gut Microbiome ◽

Cardiometabolic Risk ◽

Microbial Colonization ◽

Cardiometabolic Disease ◽

Metabolic Dysfunction ◽

Microbiome Composition ◽

Infancy And Childhood ◽

Potential Impact ◽

And Function

Emerging evidence suggests that microbiome composition and function is associated with development of obesity and metabolic disease. Microbial colonization expands rapidly following birth, and microbiome composition is particularly variable during infancy. Factors that influence the formation of the gut microbiome during infancy and childhood may have a significant impact on development of obesity and metabolic dysfunction, with life-long consequences. In this review, we examine the determinants of gut microbiome composition during infancy and childhood, and evaluate the potential impact on obesity and cardiometabolic risk.

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Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)—Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo (Gallus gallus)

Nutrients ◽

10.3390/nu10121970 ◽

2018 ◽

Vol 10 (12) ◽

pp. 1970 ◽

Cited By ~ 15

Author(s):

Desirrê Dias ◽

Nikolai Kolba ◽

Dana Binyamin ◽

Oren Ziv ◽

Marilia Regini Nutti ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Gallus Gallus ◽

Bacterial Populations ◽

Microbiome Composition ◽

Treatment Groups ◽

Micronutrient Concentration ◽

Total Body ◽

And Function

Biofortification aims to improve the micronutrient concentration and bioavailability in staple food crops. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification are scarce. In this study, we performed a 6-week feeding trial in Gallus gallus (n = 15), aimed to investigate the Fe status and the alterations in the gut microbiome following the administration of Fe-biofortified carioca bean based diet (BC) versus a Fe-standard carioca bean based diet (SC). The tested diets were designed based on the Brazilian food consumption survey. Two primary outcomes were observed: (1) a significant increase in total body Hb-Fe values in the group receiving the Fe-biofortified carioca bean based diet; and (2) changes in the gut microbiome composition and function were observed, specifically, significant changes in phylogenetic diversity between treatment groups, as there was increased abundance of bacteria linked to phenolic catabolism, and increased abundance of beneficial SCFA-producing bacteria in the BC group. The BC group also presented a higher intestinal villi height compared to the SC group. Our results demonstrate that the Fe-biofortified carioca bean variety was able to moderately improve Fe status and to positively affect the intestinal functionality and bacterial populations.

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Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

The Journal of Lipid Research ◽

10.1194/jlr.ra120000950 ◽

2020 ◽

pp. jlr.RA120000950 ◽

Cited By ~ 1

Author(s):

Min-Ting Lee ◽

Henry H Le ◽

Elizabeth L Johnson

Keyword(s):

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Dietary Lipids ◽

Rrna Gene ◽

Microbiome Composition ◽

Bioorthogonal Labeling ◽

Comparative Metabolomics ◽

Metabolic Activities ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

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Supplementation of Geranylgeraniol and Tocotrienols to High-Fat Diet Shifts the Gut Microbiome Composition and Function in Type 2 Diabetic Mice

Current Developments in Nutrition ◽

10.1093/cdn/nzaa045_026 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 393-393

Author(s):

Moamen Elmassry ◽

Eunhee Chung ◽

Abdul Hamood ◽

Chwan-Li Shen

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

High Fat Diet ◽

Alpha Diversity ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Microbiome Composition ◽

And Function

Abstract Objectives In recent years, characterization of gut microbiota composition and function were linked to the progression of type 2 diabetes mellitus. Recent evidence showed that Geranylgeraniol, an isoprenoid found in fruits, vegetables, and grains, improves glucose homeostasis. Similarly, Tocotrienols, a subfamily of vitamin E, also contains anti-diabetic properties. In this study, we examined the combined effect of geranylgeraniol and tocotrienols on the composition and function of gut microbiome in obese male mice. Methods Forty male C57BL/6J mice were assigned to 4 groups in a factorial design as follows: high-fat diet (HFD) (control group), HFD + geranylgeraniol [400 mg/kg diet] (GG group), HFD + tocotrienols [400 mg/kg diet] (TT group), and HFD + geranylgeraniol + tocotrienols (G + T group) for 14 weeks. 16S rRNA gene sequencing was done from cecal samples and microbiome and data analysis was performed with QIIME2 and PICRUSt2. Results Across all groups, the most abundant phyla were Verrucomicrobia, Firmicutes, Bacteroidetes, and Actinobacteria. There was no difference in alpha diversity among different groups. Different treatments influenced the relative abundance of certain bacteria. In the Bacteroidetes phylum, the relative abundance of family S24–7 increased in the TT group only. In the Firmicutes phylum, the relative abundance of family Lachnospiraceae was reduced upon the supplementation of geranylgeraniol or tocotrienols; individually or in combination. In Verrucomicrobia phylum, Akkermansia muciniphila relative abundance was reduced in the TT group but increased in the G + T group. The results of functional profiling of the gut microbiome revealed that geranylgeraniol supplementation caused an increase in the proportion of biosynthetic pathways related to purine, pyrimidine, and inosine-5’-phosphate and hexitol fermentation, and a decrease in the proportion of pathways involved in the biosynthesis of isoleucine, valine, histidine, arginine, and chorismate. The G + T group increased pathways related to thiamine diphosphate biosynthesis, and decreased others involved into sulfur oxidation and methylerythritol phosphate. Conclusions The influence of geranylgeraniol and tocotrienols supplementation on gut microbiome composition and function, suggests a prebiotic potential for the potential of geranylgeraniol and tocotrienols. Funding Sources American River Nutrition, LLC, Hadley, MA.

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