scholarly journals Dietary sphinganine is selectively assimilated by members of the gut microbiome

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.

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

2020 ◽  
pp. jlr.RA120000950 ◽  
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.

Alterations of gut microbiome in patients with type 2 diabetes mellitus who had undergone cholecystectomy

2021 ◽  
Vol 320 (1) ◽  
pp. E113-E121
Author(s):  
Bin Wei ◽  
Yakun Wang ◽  
Shoukui Xiang ◽  
Yan Jiang ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
New Onset

The gut microbiome of long-term T2DM patients who had undergone cholecystectomy and age- and/or sex-matched subjects of new-onset and long-term T2DM without cholecystectomy was assessed using 16S rRNA gene sequencing in stool samples. The findings suggest that, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of gut microbiome composition and function.

scholarly journals Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Góngora ◽  
Kyle H. Elliott ◽  
Lyle Whyte
Keyword(s):  
Gut Microbiome ◽  
Sulfur Isotopes ◽  
Trophic Position ◽  
Isotope Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Uria Lomvia ◽  
Fecal Microbiome ◽  
Prey Specialization ◽  
Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

Abstract 18: Gut Microbiome Modifies the Protective Effects of a Mediterranean Dietary Pattern Against Diabetes Mellitus in US Hispanics/ Latinos: The Hispanic Community Health Study/ Study of Latinos (HCHS/SOL)

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Dong Wang ◽  
Qibin Qi ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Health Study ◽  
Rrna Gene ◽  
Inverse Association ◽  
Protective Effects ◽  
Acid Fermentation ◽  
Microbiome Composition

Introduction: Little is known about whether the effect of a healthy diet on diabetes mellitus (DM) is modified by the gut microbiome in human. Hypothesis: We hypothesize that the gut microbiome modifies the inverse association between the Mediterranean diet (MedDiet) and risk of DM. Methods: This study included 543 DM cases, 805 with impaired glucose tolerance (IGT) and 394 with normal glucose regulation (NGR) in adults 23-83yrs old from the HCHS/SOL. Fecal samples were profiled using 16s rRNA gene sequencing. We applied QIIME 2 to cluster sequences into OTUs and assign taxonomies, and PICRUSt to predict metagenomic gene functions. Adherence to the MedDiet was evaluated by a MedDiet index using the average of two 24-hr dietary recalls. We applied MaAsLin2 to quantify associations between the MedDiet index and microbial features with adjustment for confounding factors listed in the caption of Fig. 1. Results: MedDiet was associated with phylogenetically diverse, rare, and abundant gut microbes (Fig. 1a). For example, a higher MedDiet index was associated with a higher relative abundance of Faecalibacterium Prausnitzii [FDR-adjusted p (q) =0.002], but a lower relative abundance of Collinsella aerofaciens ( q =0.009). We found that several microbial functions related to plant-derived polysaccharide degradation such as fructuronate reductase ( q =0.02), and short-chain fatty acid fermentation such as butyryl-CoA dehydrogenase ( q =0.002) were enriched in participants with higher MedDiet index. We found that the inverse association between MedDiet and risk of DM was more pronounced in participants with greater abundance of Prevotella copri , but weaker in participants whose gut microbial communities were dominated by Bacteroides ( P interaction =0.02 for IGT/DM vs NGR, Fig. 1b). Conclusions: Adherence to the MedDiet is associated with diverse gut microorganisms and microbial functions. The inverse association between MedDiet and risk of DM might be modified by gut microbiome composition. 1

scholarly journals Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis

Nutrients ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1874 ◽  
Author(s):  
Angela Horvath ◽  
Marija Durdevic ◽  
Bettina Leber ◽  
Katharina di Vora ◽  
Florian Rainer ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Controlled Trial ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Beneficial Effects ◽  
Compensated Cirrhosis ◽  
Gut Barrier Function ◽  
Probiotic Treatment

Probiotics have been used in trials to therapeutically modulate the gut microbiome and have shown beneficial effects in cirrhosis. However, their effect on the microbiome of cirrhosis patients is not fully understood yet. Here, we tested the effects of a multispecies probiotic on microbiome composition in compensated cirrhosis. The gut microbiome composition of 58 patients with compensated cirrhosis from a randomized controlled trial who received a daily dose of multispecies probiotics or placebo for six months was analysed by 16S rRNA gene sequencing. Microbiome composition of patients who received probiotics was enriched with probiotic strains and the abundance of Faecalibacterium prausnitzii, Syntrophococcus sucromutans, Bacteroides vulgatus, Alistipes shahii and a Prevotella species was increased in the probiotic group compared to the placebo group. Patients who had microbiome changes in response to probiotic treatment also showed a significant increase in neopterin and a significant decrease in faecal zonulin levels after intervention, which was not observed in placebo-treated patients or patients with unchanged microbiome compositions. In conclusion, multispecies probiotics may enrich the microbiome of compensated cirrhotic patients with probiotic bacteria during a six-month intervention and beneficially change the residential microbiome and gut barrier function.

scholarly journals Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
O. H. Oduaran ◽  
F. B. Tamburini ◽  
V. Sahibdeen ◽  
R. Brewster ◽  
F. X. Gómez-Olivé ◽  
...  
Keyword(s):  
South African ◽  
Gut Microbiome ◽  
Geographical Location ◽  
16S Rrna Gene Sequencing ◽  
Overweight And Obesity ◽  
Future Research ◽  
Epidemiological Transition ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Targeted Interventions

Abstract Background Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. Results We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = − 4.7). Conclusions Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

scholarly journals The Effect of Transitioning between Feeding Methods on the Gut Microbiota Dynamics of Yaks on the Qinghai–Tibet Plateau

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1641
Author(s):  
Xiao-Ling Zhang ◽  
Tian-Wei Xu ◽  
Xun-Gang Wang ◽  
Yuan-Yue Geng ◽  
Hong-Jin Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Adaptation Period ◽  
Class Level ◽  
Feeding Methods ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community ◽  
Qinghai Tibet Plateau

Here we aimed to explore the change in yak gut microbiota after transferring yaks from grazing grassland to a feedlot, and determine their diet adaptation period. Five yaks were transferred from winter pasture to an indoor feedlot. Fecal samples were obtained from grazing (G) and feedlot feeding yaks at day 1 (D1), day 4 (D4), day 7 (D7), day 11 (D11), and day 16 (D16). The dynamic variation of the bacterial community was analyzed using 16S rRNA gene sequencing. The results showed that the yak gut microbial community structure underwent significant changes after diet transition. At the phylum and genus levels, most bacteria changed within D1–D11; however, no significant changes were observed from D11–D16. Furthermore, we used random forest to determine the key bacteria (at class level) disturbing gut micro-ecology. The relative abundance of the top four classes (Erysipelotrichia, Gammaproteobacteria, Saccharimonadia, and Coriobacteriia) was highest on D1–D4, and then decreased and plateaued over time. Our results demonstrated that an abrupt adjustment to a diet with high nutrition could influence the gut micro-ecology, which was stabilized within 16 days, thus providing insights into diet adaptation in the yak gut.

scholarly journals Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽  
2019 ◽  
Vol 14 (2) ◽  
pp. e0212474 ◽  
Author(s):  
Daniel E. Almonacid ◽  
Laurens Kraal ◽  
Francisco J. Ossandon ◽  
Yelena V. Budovskaya ◽  
Juan Pablo Cardenas ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Reference Ranges ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Rrna Gene Sequencing

scholarly journals The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Wei Song ◽  
Lingzhi Li ◽  
Hongliang Huang ◽  
Keji Jiang ◽  
Fengying Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Antarctic Fish ◽  
16S Rrna Gene Sequencing ◽  
Physiological Characteristics ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

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