Distinct Features of Gut Microbiota in High-Altitude Tibetan and Middle-Altitude Han Hypertensive Patients

Indigenous animals show unique gut microbiota (GM) in the Tibetan plateau. However, it is unknown whether the hypertensive indigenous people in plateau also have the distinct gut bacteria, different from those living in plains. We sequenced the V3-V4 region of the gut bacteria 16S ribosomal RNA (rRNA) gene of feces samples among hypertensive patients (HPs) and healthy individuals (HIs) from 3 distinct altitudes: Tibetans from high altitude (3600–4500 m, n = 38 and 34), Hans from middle altitude (2260 m, n = 49 and 35), and Hans from low altitude (13 m, n = 34 and 35) and then analyzed the GM composition among hypertensive and healthy subgroups using the bioinformatics analysis, respectively. The GM of high-altitude Tibetan and middle-altitude Han HPs presented greater α- and β-diversities, lower ratio of Firmicutes/Bacteroidetes (F/B), and higher abundance of beneficial Verrucomicrobia and Akkermansia than the low-altitudes HPs did. The GM of high-altitude Tibetan and middle-altitude HIs showed greater α-diversity and lower ratio of F/B than the low-altitudes HIs did. But, β-diversity and abundance of Verrucomicrobia and Akkermansia among different subgroups of HIs did not show any differences. Conclusively, the high-altitude Tibetan and middle-altitude Han HPs have a distinct feature of GM, which may be important in their adaptation to hypertension in the plateau environments.

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Impact of Vitamin D Deficit on the Rat Gut Microbiome

Nutrients ◽

10.3390/nu11112564 ◽

2019 ◽

Vol 11 (11) ◽

pp. 2564 ◽

Cited By ~ 2

Author(s):

Iñaki Robles-Vera ◽

María Callejo ◽

Ricardo Ramos ◽

Juan Duarte ◽

Francisco Perez-Vizcaino

Keyword(s):

Vitamin D ◽

Gut Microbiota ◽

Vitamin D Deficiency ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbiome Composition ◽

Gut Dysbiosis ◽

Β Diversity ◽

Α Diversity ◽

Rat Gut

Inadequate immunologic, metabolic and cardiovascular homeostasis has been related to either an alteration of the gut microbiota or to vitamin D deficiency. We analyzed whether vitamin D deficiency alters rat gut microbiota. Male Wistar rats were fed a standard or a vitamin D-free diet for seven weeks. The microbiome composition was determined in fecal samples by 16S rRNA gene sequencing. The vitamin D-free diet produced mild changes on α- diversity but no effect on β-diversity in the global microbiome. Markers of gut dysbiosis like Firmicutes-to-Bacteroidetes ratio or the short chain fatty acid producing bacterial genera were not significantly affected by vitamin D deficiency. Notably, there was an increase in the relative abundance of the Enterobacteriaceae, with significant rises in its associated genera Escherichia, Candidatus blochmannia and Enterobacter in vitamin D deficient rats. Prevotella and Actinomyces were also increased and Odoribacteraceae and its genus Butyricimonas were decreased in rats with vitamin D-free diet. In conclusion, vitamin D deficit does not induce gut dysbiosis but produces some specific changes in bacterial taxa, which may play a pathophysiological role in the immunologic dysregulation associated with this hypovitaminosis.

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Taxonomic composition and diversity of the gut microbiota in relation to habitual diet in Korean adults

10.21203/rs.2.22869/v1 ◽

2020 ◽

Author(s):

Hwayoung Noh ◽

Hwan-Hee Jang ◽

Gichang Kim ◽

Semi Zouiouich ◽

Su-Yeon Cho ◽

...

Keyword(s):

Gut Microbiota ◽

Smoking Status ◽

Taxonomic Composition ◽

Alcoholic Beverages ◽

Rrna Gene ◽

Fermented Foods ◽

Korean Adults ◽

Β Diversity ◽

Α Diversity ◽

Habitual Diet

Abstract Background: Little is known of the relationship between the Korean habitual diet and gut microbiota composition. We investigated associations of habitual dietary intake of foods and nutrients with the taxonomic composition and diversity of gut microbiota in 222 Korean adults aged 18-58 years in a cross-sectional study. Gut microbial taxonomic composition and diversity data were obtained by 16S rRNA gene sequencing of bacterial DNA extracted from fecal samples. Habitual diet for the previous year was collected by a validated food frequency questionnaire. Correlations between intakes of food and nutrients and gut microbial taxonomic composition were examined with adjustment for sex, age, body mass index, dietary supplement, smoking status, and sample batch. Specific dietary patterns associated with α-diversity were identified by reduced rank regression. Enterotypes of gut microbiota were explored by principal coordinate analysis based on β-diversity.Results: The intakes of vegetables, fermented legumes, and potatoes were positively associated with the Firmicutes-to-Bacteroidetes (F/B) ratio, while the intakes of noodle products and non-alcoholic beverages were inversely related to the F/B ratio (all P<0.05). A dietary pattern associated with higher α-diversity (HiαDP) was characterized by greater intakes of fermented legumes, vegetables, potatoes, tea, and fruit/fruit juice and lower intakes of non-alcoholic beverages. Among three different enterotypes identified based on the β-diversity, the Ruminococcus enterotype had higher scores of the HiαDP and was more strongly associated with intakes of vegetables and nuts/seeds, compared to the two other enterotypes. Conclusions: We conclude that the habitual diet in Korean adults was associated with gut microbial taxonomic composition and diversity. A higher intake of plant-based and fermented foods was associated with distinct gut microbial enterotypes in Korean adults.

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A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study

Nutrients ◽

10.3390/nu13051682 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1682

Author(s):

Ewa Łoś-Rycharska ◽

Marcin Gołębiewski ◽

Marcin Sikora ◽

Tomasz Grzybowski ◽

Marta Gorzkiewicz ◽

...

Keyword(s):

Atopic Dermatitis ◽

Food Allergy ◽

Gut Microbiota ◽

Bacterial Species ◽

Rrna Gene ◽

Healthy Children ◽

Skin Microbiota ◽

Fecal Samples ◽

Healthy Infants ◽

Α Diversity

The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patients with allergies, hence simultaneous analysis of the two compartments of microbiota was performed in infants with and without allergic symptoms. Fifty-nine infants with food allergy and/or atopic dermatitis and 28 healthy children were enrolled in the study. The skin and gut microbiota were evaluated using 16S rRNA gene amplicon sequencing. No significant differences in the α-diversity of dermal or fecal microbiota were observed between allergic and non-allergic infants; however, a significant relationship was found between bacterial community structure and allergy phenotypes, especially in the fecal samples. Certain clinical conditions were associated with characteristic bacterial taxa in the skin and gut microbiota. Positive correlations were found between skin and fecal samples in the abundance of Gemella among allergic infants, and Lactobacillus and Bacteroides among healthy infants. Although infants with allergies and healthy infants demonstrate microbiota with similar α-diversity, some differences in β-diversity and bacterial species abundance can be seen, which may depend on the phenotype of the allergy. For some organisms, their abundance in skin and feces samples may be correlated, and these correlations might serve as indicators of the host’s allergic state.

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Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa141 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Robert Lavallée ◽

Claude Guertin

Keyword(s):

Population Density ◽

Gut Microbiome ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Economic Damage ◽

Taxonomic Structure ◽

Rrna Gene ◽

Local Conditions ◽

Β Diversity ◽

Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

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The effects of gestational age on the composition and predicted function of gut microbiota in neonates and early infants

World Journal of Advanced Research and Reviews ◽

10.30574/wjarr.2021.12.2.0648 ◽

2021 ◽

Vol 12 (2) ◽

pp. 567-573

Author(s):

Kaiyu Pan ◽

Lianfang Yu ◽

Chengyue Zhang ◽

Jianhua Zhan ◽

Rongliang Tu

Keyword(s):

Gut Microbiota ◽

Gestational Age ◽

Full Term ◽

Rrna Gene ◽

Delivery Mode ◽

16S Sequencing ◽

Α Diversity ◽

Preterm Group ◽

Stool Samples ◽

Predicted Function

Gut microbiota can influence cell differentiation, metabolism, and immune function and is key for the normal development and future health of early infants. Several factors have been reported to be related to the microbiota composition of neonates, such as gestational age, delivery mode, feeding method, antibiotics consumption, and ethnicity, among others. So we investigated the relationship between gestational age and the composition and predicted function of the gut microbiota of neonates and early infants by sequencing the 16S rRNA gene present in stool samples obtained from 100 prospectively enrolled full-term and preterm newborns. In the 3-day-old neonates samples, the prominent genera in the full-term group were Escherichia-Shigella, Streptococcus, Bifidobacterium, and Bacteroides, while in the preterm group, Staphylococcus, Streptococcus, Escherichia-Shigella and Clostridium were the most abundant genera identified. There were statistical difference between two groups(P<0.05). Moreover, the predominant genera in the full-term group were Bifidobacterium, Lactobacillus, Bacteroides, and Clostridium , whereas the main genera in the preterm group were Escherichia-Shigella, Clostridium, Bifidobacterium and Bacteroides, in stool samples from 30-42-day-old infants. We found the α-diversity in 3-day-old group was significantly lower than in the 30-42-day-old group whether it’s full-term or preterm (P<0.001). Functional inference analysis revealed higher levels of biodegradation and metabolism of carbohydrates, vitamins in the full-term group than in the preterm group, both in neonates and early infants, which may contribute to the stability of the microbiota in the full-term group. There were significant differences in the composition and predicted function of the gut microbiota of early infants due to gestational age. The 16S sequencing technology was an effective and reliable tool in the detection of gut microbiota in early infants.

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Pilot trial of vitamin D3 and calcifediol in healthy vitamin D deficient adults: does it change the fecal microbiome?

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/clinem/dgab573 ◽

2021 ◽

Author(s):

Albert Shieh ◽

S Melanie Lee ◽

Venu Lagishetty ◽

Carter Gottleib ◽

Jonathan P Jacobs ◽

...

Keyword(s):

Vitamin D ◽

Vitamin D Deficiency ◽

Relative Abundance ◽

Vitamin D3 ◽

Pilot Trial ◽

Fecal Microbiota ◽

Small Sample ◽

Rrna Gene ◽

Β Diversity ◽

Α Diversity

Abstract Purpose To determine whether correcting vitamin D deficiency with cholecalciferol (vitamin D3, D3) or calcifediol (25-hydroxyvitamin D3, 25(OH)D3) changes gut microbiome composition. Methods 18 adults with vitamin D deficiency (25-hydroxyvitamin D [25(OH)D] <20 ng/ml) received 60 mcg/day of D3 or 20 mcg/day of 25(OH)D3 for 8 weeks. Changes in serum 25(OH)D, 1,25-diydroxyvitamin D (1,25(OH)2D), and 24,25-dihydroxyvitamin D (24,25(OH)2D) were assessed. We characterized composition of the fecal microbiota using 16S rRNA gene sequencing, and examined changes in α-diversity (Chao 1, Faith’s Phylogenetic Diversity, Shannon Index), β-diversity (DEICODE), and genus-level abundances (DESeq2). Results Vitamin D3 and 25(OH)D3 groups were similar. After 8 weeks of vitamin D3, mean 25(OH)D and 24,25(OH)2D increased significantly, but 1,25(OH)2D did not (25(OH)D: 17.8 to 30.1 ng/ml [p=0.002]; 24,25(OH)2D: 1.1 to 2.7 ng/ml [p=0.003]; 1,25(OH)2D: 49.5 to 53.0 pg/ml [p=0.9]). After 8 weeks of 25(OH)D3, mean 25(OH)D, 24,25(OH)2D, and 1,25(OH)2D increased significantly (25(OH)D: 16.7 to 50.6 ng/ml [p<0.0001]; 24,25(OH)2D: 1.3 to 6.2 ng/ml [p=0.0001]; 1,25(OH)2D: 56.5 to 74.2 pg/ml [p=0.05]). Fecal microbial α-diversity and β-diversity did not change with D3 or 25D3 supplementation. Mean relative abundance of Firmicutes increased and mean relative abundance of Bacterioidetes decreased from baseline to four weeks, but returned to baseline by study completion. DESeq2 analysis did not confirm any statistically significant taxonomic changes. Main conclusions In a small sample of healthy adults with vitamin D deficiency, restoration of vitamin D sufficiency with vitamin D3 or 25(OH)D3 did not lead to lasting changes in the fecal microbiota.

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Association of subjective global assessment of nutritional status with gut microbiota in hemodialysis patients: a case–control study

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfaa019 ◽

2020 ◽

Cited By ~ 2

Author(s):

Ting-Yun Lin ◽

Szu-Chun Hung

Keyword(s):

Nutritional Status ◽

Gut Microbiota ◽

Global Assessment ◽

Hemodialysis Patients ◽

Adverse Outcomes ◽

Subjective Global Assessment ◽

Protein Energy Wasting ◽

Β Diversity ◽

Protein Energy ◽

Α Diversity

Abstract Background Protein-energy wasting (PEW) is prevalent and associated with adverse outcomes in patients with chronic kidney disease (CKD). However, the pathogenesis of PEW in CKD patients has not been fully identified. The gut microbiota has been implicated in the regulation of host metabolism and energy balance. Therefore, we aimed to explore the association between nutritional status and the composition of the gut microbiota in hemodialysis patients. Methods Gut microbial diversity and taxonomy were examined in 88 hemodialysis patients with PEW (n = 22) and normal nutritional status (n = 66) who were matched 1:3 for age and sex. Nutritional status was assessed by using the 7-point subjective global assessment (SGA) score (1–3 = severe PEW; 4–5 = moderate PEW and 6–7 = normal nutrition). The gut microbiota was assessed by 16S ribosomal RNA gene sequencing. Results Patients with normal nutritional status had a significantly higher body mass index and physical activity and serum albumin levels, but significantly lower levels of inflammatory cytokines than patients with PEW. The most striking finding was that the α-diversity of the gut microbiota was significantly lower in patients with PEW. In a multivariate analysis, the SGA score was independently and positively associated with α-diversity (P = 0.049). Patients with or without PEW were different with respect to the principal coordinate analysis of β-diversity. Notably, the relative abundance of Faecalibacterium prausnitzii, a butyrate-producing bacteria, was markedly reduced in patients with PEW. Conclusion In hemodialysis patients, PEW assessed with the SGA was associated with gut dysbiosis.

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Ongoing Supplementation of Probiotics to Cesarean-Born Neonates during the First Month of Life may Impact the Gut Microbial

American Journal of Perinatology ◽

10.1055/s-0040-1710559 ◽

2020 ◽

Cited By ~ 1

Author(s):

Wenqing Yang ◽

Liang Tian ◽

Jiao Luo ◽

Jialin Yu

Keyword(s):

Gut Microbiota ◽

Intestinal Microbiota ◽

Influencing Factor ◽

Delivery Mode ◽

Next Generation Sequencing Technology ◽

Operational Taxonomic Units ◽

Β Diversity ◽

Α Diversity ◽

Clusters Of Orthologous Groups ◽

And Function

Objective The delivery mode is considered to be a significant influencing factor in the early gut microbiota composition, which is associated with the long-term health of the host. In this study, we tried to explore the effects of probiotics on the intestinal microbiota of C-section neonates. Study Design Twenty-six Chinese neonates were enrolled in this study. The neonates were divided into four groups: VD (natural delivery neonates, n = 3), CD (cesarean-born neonates, n = 9), CDL (cesarean-born neonates supplemented with probiotic at a lower dosage, n = 7), and CDH (cesarean-born neonates supplemented with probiotic at a higher dosage, n = 7). Fecal samples were collected on the 3rd, 7th, and 28th day since birth. The V3–V4 region of the 16S ribosomal ribonucleic acid gene was sequenced by next-generation sequencing technology. Results The α-diversity of the intestinal microbiota of cesarean delivery neonates was significantly lower than that of the naturally delivered neonates on the 28th day (p = 0.005). After supplementation with probiotics for 28 days, the α-diversity and the β-diversity of the gut flora in the cesarean-born infants (CDL28 and CDH28) was similar to that in the vaginally delivery infants. Meanwhile, the abundances of Lactobacillus and Bifidobacterium were significantly increased since the 3rd day of probiotic supplementation. Besides, the sustained supplementation of probiotics to neonates would help improve the abundance of the operational taxonomic units in several different Clusters of Orthologous Groups of proteins. Conclusion This study showed that probiotics supplementation to cesarean-born neonates since birth might impact the diversity and function of gut microbiota. Key Points

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Microbial signature in IgE-mediated food allergies

Genome Medicine ◽

10.1186/s13073-020-00789-4 ◽

2020 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Michael R. Goldberg ◽

Hadar Mor ◽

Dafna Magid Neriya ◽

Faiga Magzal ◽

Efrat Muller ◽

...

Keyword(s):

Food Allergy ◽

Gut Microbiota ◽

Learning Algorithm ◽

Area Under The Curve ◽

Food Allergies ◽

Rrna Gene ◽

Microbiota Composition ◽

Α Diversity ◽

Ige Mediated ◽

Gut Microbiota Composition

Abstract Background Multiple studies suggest a key role for gut microbiota in IgE-mediated food allergy (FA) development, but to date, none has studied it in the persistent state. Methods To characterize the gut microbiota composition and short-chain fatty acid (SCFAs) profiles associated with major food allergy groups, we recruited 233 patients with FA including milk (N = 66), sesame (N = 38), peanut (N = 71), and tree nuts (N = 58), and non-allergic controls (N = 58). DNA was isolated from fecal samples, and 16S rRNA gene sequences were analyzed. SCFAs in stool were analyzed from patients with a single allergy (N = 84) and controls (N = 31). Results The gut microbiota composition of allergic patients was significantly different compared to age-matched controls both in α-diversity and β-diversity. Distinct microbial signatures were noted for FA to different foods. Prevotella copri (P. copri) was the most overrepresented species in non-allergic controls. SCFAs levels were significantly higher in the non-allergic compared to the FA groups, whereas P. copri significantly correlated with all three SCFAs. We used these microbial differences to distinguish between FA patients and non-allergic healthy controls with an area under the curve of 0.90, and for the classification of FA patients according to their FA types using a supervised learning algorithm. Bacteroides and P. copri were identified as taxa potentially contributing to KEGG acetate-related pathways enriched in non-allergic compared to FA. In addition, overall pathway dissimilarities were found among different FAs. Conclusions Our results demonstrate a link between IgE-mediated FA and the composition and metabolic activity of the gut microbiota.

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A game theory model for gut bacterial nutrient utilization strategies during human infancy

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.0824 ◽

2020 ◽

Vol 287 (1931) ◽

pp. 20200824 ◽

Cited By ~ 2

Author(s):

Inga Leena Angell ◽

Knut Rudi

Keyword(s):

Game Theory ◽

Gut Microbiota ◽

Nutrient Utilization ◽

Theory Model ◽

Ecological Processes ◽

Β Diversity ◽

Gut Colonization ◽

Α Diversity ◽

Colonization Patterns ◽

Expanding Population

Despite the fact that infant gut colonization patterns have been extensively studied, we have limited knowledge about the underlying ecological processes. This particularly relates to the ecological choice of nutrient utilization strategies. The aim of the current study was therefore to compare empirically determined nutrient utilization strategies with that expected from a combinatorial game theory model. Observational analyses for 100 mother–child pairs suggested mother–child transmission of specialists with the potential to use few nutrients. Generalists, on the other hand, with the potential to use many nutrients, peaked at three months of age for the children. The level of generalists was gradually replaced with specialists up to 12 months of age. Game theory simulation revealed a competitive advantage of generalists in an expanding population, while more specialized bacteria were favoured with the maturation of the population. This suggests that the observed increase in generalists in the three-month-old children could be due to an immature, expanding gut microbiota population while the increase of specialists at 12 months could be due to population maturation. The simulated and empirical data also correspond with respect to an increased α diversity and a decreased β diversity with the number of simulations and age, respectively. Taken together, game theory simulation of nutrient utilization strategies can therefore provide novel insight into the maturation of the human gut microbiota during infancy.

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