Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19)

Abstract Objectives 1. To characterize the gut microbiome and 2. explore associations between dietary intake and gut microbiome composition and predicted function among children at screening for participation in a randomized controlled feeding trial in urban slums of Mumbai, India. Methods Young children (10–18 months old) living in urban slums of Mumbai were screened from March to November 2017 after obtaining informed consent from caregivers. Nutrient intakes from 24-hour dietary recall were analyzed as absolute intakes, % of RDA, and using the nutrient residual to adjust for energy intake. DNA extracted from rectal swabs was sequenced (16S rRNA V3-V4 region; Illumina MiSeq) and further processed using QIIME2 and PICRUSt algorithm. Linear regression was used to estimate associations between nutrient intakes (adjusted for age and sex) and measures of gut microbiome α-diversity, including Shannon Index, Chao1 estimator, observed OTUs, Proteobacteria relative abundance, Firmicutes: Bacteroidetes ratio, and predicted KEGG pathways. Statistical analysis was performed using RStudio, and SAS 9.4. Results A subset of 53 children with rectal swabs collected were included. Sequencing yielded 8984,126 reads including 2173 unique operational taxonomic units (OTUs). Mean relative abundance of Proteobacteria was 78.2%. Shannon Diversity Index was positively associated with absolute intakes of total carotenoids and beta-carotene. Children with adequate intakes of zinc and beta-carotene had a higher mean Shannon Diversity Index. The Chao1 estimator was positively associated with absolute intakes of calcium. The number of observed OTUs was positively associated with calcium and zinc intakes. The predicted gene counts for germination, sporulation, amoebiasis, and protein digestion and absorption pathways were also associated with both macro- and micro-nutrient intakes. Conclusions The gut microbiome in this sample of young children in Mumbai was dominated by Proteobacteria, which includes many potentially pathogenic species. Dietary intakes of macro- and micronutrients were associated with measures of diversity and predicted functional pathways after adjustment for age and sex, warranting further longitudinal study of the diet's impact on the microbiome particularly in young children. Funding Sources HarvestPlus.

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Diversity and Abundance of Insects at the Campus of Higher Polytechnic Institute of Manica, Mozambique

Asian Journal of Research in Zoology ◽

10.9734/ajriz/2021/v4i130106 ◽

2021 ◽

pp. 34-39

Author(s):

António C. Manhice

Keyword(s):

Relative Abundance ◽

Diversity Index ◽

Polytechnic Institute ◽

Shannon Diversity Index ◽

Sampling Techniques ◽

Insect Diversity ◽

Pitfall Traps ◽

Shannon Diversity ◽

Diversity Sampling

The aim of this study was to assess insect diversity and abundance at the Campus of Higher Polytechnic Institute of Manica, Mozambique. Collection of insects was carried out by pitfall traps a long linear transects and sweep nets during 21 days of October 2019. Data were analyzed using descriptive statistical and Shannon diversity index. A total of 1780 individuals of insects belonging to 8 orders, 15 families and 27 species were collected. Highest relative abundance was observed in Hymenoptera order (92.64%), and the least were Blattodea (2.70%), Diptera (2.13%), Coleoptera (0.82%), Orthoptera (1.52%), Phasmatodea (0.06%), Mantodea (0.28%) and Hemiptera (0.11%). The abundant specie was Crematogaster peringueyi (Hymenoptera) with 89.83% follwed by Macrotermes natalensis (Blattodea) and Chrysonmya chloropyga (Diptera) with 2.47% and 1.63% respectively. Higher insect diversity was observed in Orthoptera order (Shannon, H'=1.76), while the orders Coleoptera, Diptera, Hymenoptera, Blattodea, Phasmatodea, Hemiptera, had the lowest diversity (Shannon, H'<1). Further work need to be done in the study area, expanding the duration of the study and applying diversity sampling techniques.

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Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels

Scientific Reports ◽

10.1038/s41598-019-51698-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Denise C. Zysset-Burri ◽

Irene Keller ◽

Lieselotte E. Berger ◽

Peter J. Neyer ◽

Christian Steuer ◽

...

Keyword(s):

Cardiovascular Disease ◽

Relative Abundance ◽

Negative Correlation ◽

Gut Microbiome ◽

Cholesterol Metabolism ◽

Retinal Artery Occlusion ◽

Artery Occlusion ◽

Metabolism Pathway ◽

Retinal Artery ◽

Age And Sex

Abstract Retinal artery occlusion (RAO) is a sight threatening complication of cardiovascular disease and commonly occurs due to underlying atherosclerosis. As cardiovascular disease and atherosclerosis in particular has been associated with compositional alterations in the gut microbiome, we investigated this association in patients with clinically confirmed non-arteritic RAO compared to age- and sex-matched controls. On the phylum level, the relative abundance of Bacteroidetes was decreased in patients with RAO compared to controls, whereas the opposite applied for the phylum of Proteobacteria. Several genera and species such as Actinobacter, Bifidobacterium spp., Bacteroides stercoris, Faecalibacterium prausnitzii were relatively enriched in patients with RAO, whereas others such as Odoribacter, Parasutterella or Lachnospiraceae were significantly lower. Patient’s gut microbiomes were enriched in genes of the cholesterol metabolism pathway. The gut derived, pro-atherogenic metabolite trimethylamine-N-oxide (TMAO) was significantly higher in patients with RAO compared to controls (p = 0.023) and a negative correlation between relative abundances of genera Parasutterella and Lachnospiraceae and TMAO levels and a positive correlation between relative abundance of genus Akkermansia and TMAO levels was found in study subjects. Our findings proposes that RAO is associated with alterations in the gut microbiome and with elevated TMAO levels, suggesting that RAO could be targeted by microbiome-altering interventions.

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Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus

PLoS ONE ◽

10.1371/journal.pone.0251245 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251245

Author(s):

Amanda K. Kitten ◽

Laurajo Ryan ◽

Grace C. Lee ◽

Bertha E. Flores ◽

Kelly R. Reveles

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Relative Abundance ◽

Gut Microbiome ◽

Beta Diversity ◽

Mexican Americans ◽

Public Health Problem ◽

Shannon Diversity

Purpose Type 2 diabetes mellitus (T2DM) is an urgent public health problem and disproportionately affects Mexican Americans. The gut microbiome contributes to the pathophysiology of diabetes; however, no studies have examined this association in Mexican-Americans. The objective of this study was to compare gut microbiome composition between Mexican-Americans with and without T2DM. Methods This was a cross-sectional study of volunteers from San Antonio, TX. Subjects were 18 years or older and self-identified as Mexican American. Subjects were grouped by prior T2DM diagnosis. Eligible subjects attended a clinic visit to provide demographic and medical information. Thereafter, subjects recorded their dietary intake for three days and collected a stool sample on the fourth day. Stool 16s rRNA sequences were classified into operational taxonomic units (OTUs) via the mothur bayesian classifier and referenced to the Greengenes database. Shannon diversity and bacterial taxa relative abundance were compared between groups using the Wilcoxon rank sum test. Beta diversity was estimated using Bray-Curtis indices and compared between groups using PERMANOVA. Results Thirty-seven subjects were included, 14 (38%) with diabetes and 23 (62%) without diabetes. Groups were well-matched by body mass index and comorbid conditions. Shannon diversity was not significantly different between those with and without T2DM (3.26 vs. 3.31; p = 0.341). Beta diversity was not significantly associated with T2DM diagnosis (p = 0.201). The relative abundance of the most common bacterial phyla and families did not significantly differ between groups; however, 16 OTUs were significantly different between groups. Conclusions Although alpha diversity was not significantly different between diabetic and non-diabetic Mexican Americans, the abundance of certain bacterial taxa were significantly different between groups.

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The Denser Canopy of Mangrove Drives the Structure of Insect Communities

Tropical Life Sciences Research ◽

10.21315/tlsr2020.31.3.6 ◽

2020 ◽

Vol 31 (3) ◽

pp. 77-90

Author(s):

Yendra Pratama Setyawan ◽

Wakhid Wakhid ◽

Suhadi Suhadi

Keyword(s):

Relative Abundance ◽

Diversity Index ◽

Canopy Cover ◽

Abundant Species ◽

Mangrove Ecosystem ◽

Shannon Diversity Index ◽

Shannon Diversity ◽

Evenness Index ◽

Age Variation ◽

Richness Index

Mangrove restoration in Trenggalek, East Java has resulted an age variation of mangrove ecosystem. Diverse species of insects predominantly found in mangroves were collected using yellow pan traps, swipe nets and by direct picking from three different sites. This research was conducted from April until August 2015. There are 9,181 individual insects associated with mangroves comprised of 42 species from 31 families and eight orders. The first site or the 15 years old mangrove (66.22% canopy cover) indicated the highest Shannon diversity index at 2.54, Evenness index of 0.32 and Margalef richness index of 4.84. The lowest diversity was recorded in the third site or the five years old mangrove (19.65% canopy cover), with the Shannon diversity index at 2.28, Evenness index at 0.26 and Margalef richness index at 4.59. The most abundant species located was the Eristena mangalis, with 1,724 individuals (relative abundance of 18.78%), followed by Monolepta sp. with 1,649 individuals (relative abundance of 17.96%). These are the phytophagous insects associated with mangrove leaves. This study concluded that the older mangrove ecosystem have a denser canopy that supports insect life.

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Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

Journal of Personalized Medicine ◽

10.3390/jpm11040294 ◽

2021 ◽

Vol 11 (4) ◽

pp. 294

Author(s):

Irina Grigor’eva ◽

Tatiana Romanova ◽

Natalia Naumova ◽

Tatiana Alikina ◽

Alexey Kuznetsov ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Gallstone Disease ◽

Illumina Miseq ◽

Rrna Gene ◽

Bacterial Phyla ◽

Female Patients ◽

Composition And Structure ◽

Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

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On a Variational Definition for the Jensen-Shannon Symmetrization of Distances Based on the Information Radius

Entropy ◽

10.3390/e23040464 ◽

2021 ◽

Vol 23 (4) ◽

pp. 464

Author(s):

Frank Nielsen

Keyword(s):

Diversity Index ◽

Diversity Indices ◽

Shannon Diversity Index ◽

Probability Measures ◽

Variational Optimization ◽

Shannon Diversity ◽

Concept Of Information ◽

Jensen Shannon Divergence

We generalize the Jensen-Shannon divergence and the Jensen-Shannon diversity index by considering a variational definition with respect to a generic mean, thereby extending the notion of Sibson’s information radius. The variational definition applies to any arbitrary distance and yields a new way to define a Jensen-Shannon symmetrization of distances. When the variational optimization is further constrained to belong to prescribed families of probability measures, we get relative Jensen-Shannon divergences and their equivalent Jensen-Shannon symmetrizations of distances that generalize the concept of information projections. Finally, we touch upon applications of these variational Jensen-Shannon divergences and diversity indices to clustering and quantization tasks of probability measures, including statistical mixtures.

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Impact of the gut microbiome on the atorvastatin-dependent modulation of the serum lipidome

European Heart Journal ◽

10.1093/ehjci/ehaa946.3823 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

J Roessler ◽

F Zimmermann ◽

D Schmidt ◽

U Escher ◽

A Jasina ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Gut Microbiome ◽

Interindividual Variation ◽

Funding Source ◽

Microbial Composition ◽

Atorvastatin Treatment ◽

Qrt Pcr ◽

16S Rna ◽

Regulatory Properties

Abstract Background and aims The modulation of serum lipids, in particular of the low-density lipoprotein cholesterol (LDL-C), by statins varies between individuals. The mechanisms regulating this interindividual variation are only poorly understood. Here, we investigated the relation between the gut microbiome and the regulatory properties of atorvastatin on the serum lipidome using mice with depleted gut microbiome. Methods Over a period of 6 weeks, mice (C57BL/6) with either an intact (conventional mice, CONV, n=24) or antibiotic-based depleted gut microbiome (antibiotic treated mice, ABS, n=16) were put on standard chow diet (SCD) or high fat diet (HFD), respectively. During the last 4 weeks of treatment atorvastatin (Ator, 10mg/kg body weight/day) or control vehicle was administered via daily oral gavage. Blood lipids (total cholesterol, VLDL, LDL-C, HDL-C) and serum sphingolipids were compared among the groups. The expressions of hepatic and intestinal genes involved in cholesterol metabolism were analyzed by qRT-PCR. Alterations in the gut microbiota profile of mice with intact gut microbiome were examined using 16S RNA qRT-PCR. Results In CONV mice, HFD led to significantly increased blood LDL-C levels as compared with SCD (HFD: 36.8±1.4 mg/dl vs. SCD: 22.0±1.8 mg/dl; P<0.01). In CONV mice atorvastatin treatment significantly reduced blood LDL-C levels after HFD, whereas in ABS mice the LDL-C lowering effect of atorvastatin was markedly attenuated (CONV+HFD+Ator: 31.0±1.8 mg/dl vs. ABS+HFD+Ator: 46.4±3 mg/dl; P<0.01). A significant reduction in the abundance of several plasma lipids, in particular sphingolipids and glycerophospholipids upon atorvastatin treatment was observed in CONV mice, but not in ABS mice. The expressions of distinct hepatic and intestinal cholesterol-regulating genes (ldlr, srebp2, pcsk9 and npc1l1) upon atorvastatin treatment were significantly altered in gut microbiota depleted mice. In response to HFD a decrease in the relative abundance of the bacterial phyla Bacteroides and an increase in the relative abundance of Firmicutes was observed. The altered ratio between Bacteroides and Firmicutes in HFD fed mice was partly reversed upon atorvastatin treatment. Conclusions Our findings indicate a crucial role of the gut microbiome for the regulatory properties of atorvastatin on the serum lipidome and, in turn, support a critical impact of atorvastatin on the gut microbial composition. The results provide novel insights into potential microbiota related mechanisms underlying interindividual variation in modulation of the serum lipidome by statins, given interindividual differences in microbiome composition and function. Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): German Heart Research Foundation

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Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean

Microorganisms ◽

10.3390/microorganisms9030465 ◽

2021 ◽

Vol 9 (3) ◽

pp. 465

Author(s):

Anne A. M. J. Becker ◽

KC Hill ◽

Patrick Butaye

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

Taxonomic Diversity ◽

Caribbean Islands ◽

Microbial Profile ◽

Vegetation Zones ◽

Males And Females ◽

The Caribbean ◽

Metabolic Properties ◽

Small Indian Mongoose

Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5TM XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator’s impact throughout the Caribbean.

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Species richness and diversity in shrub savanna using ordinary kriging

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2016000800008 ◽

2016 ◽

Vol 51 (8) ◽

pp. 958-966 ◽

Cited By ~ 3

Author(s):

Anderson Pedro Bernardina Batista ◽

José Márcio de Mello ◽

Marcel Régis Raimundo ◽

Henrique Ferraço Scolforo ◽

Aliny Aparecida dos Reis ◽

...

Keyword(s):

Spatial Distribution ◽

Species Richness ◽

Spatial Dependence ◽

Ordinary Kriging ◽

Diversity Index ◽

Spatial Models ◽

Shannon Diversity Index ◽

Shannon Diversity ◽

Species Richness And Diversity ◽

Number Of Species

Abstract: The objective of this work was to analyze the spatial distribution and the behavior of species richness and diversity in a shrub savanna fragment, in 2003 and 2014, using ordinary kriging, in the state of Minas Gerais, Brazil. In both evaluation years, the measurements were performed in a fragment with 236.85 hectares, in which individual trees were measured and identified across 40 plots (1,000 m2). Species richness was determined by the total number of species in each plot, and diversity by the Shannon diversity index. For the variogram study, spatial models were fitted and selected. Then, ordinary kriging was applied and the spatial distribution of the assessed variables was described. A strong spatial dependence was observed between species richness and diversity by the Shannon diversity index (<25% spatial dependence degree). Areas of low and high species diversity and richness were found in the shrub savanna fragment. Spatial distribution behavior shows relative stability regarding the number of species and the Shannon diversity index in the evaluated years.

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