chao1 estimator
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Karstenia ◽  
2020 ◽  
pp. 292-315
Author(s):  
Yuri K. Novozhilov ◽  
Oleg N. Shchepin ◽  
Vladimir I. Gmoshinskiy ◽  
Martin Schnittler

Northern taiga forests and subalpine plant communities of the Laplandskiy State Nature Biosphere Reserve (Kola Peninsula, Russia) were surveyed for myxomycetes. A total of 1675 specimens of myxomycete fruit bodies (sporocarps) were registered, among them 1584 records from field collections and 92 obtained from 210 moist chamber cultures of ground litter, bark of living trees, wood, and weathered dung of moose and willow ptarmigan. Most of 125 taxa (124 morphospecies and one variety) representing 34 genera were recorded only in the field (104 taxa from 32 genera), but some were exclusively obtained from moist chamber cultures (8 taxa from 5 genera). All of the recorded species are new for the Laplandskiy Reserve. Species numbers decreased among the four studied forest associations along the elevation and mositure gradient, and the Shannon index showed a similar trend: spruce forest (PICa; 84 taxa, H’=3.8), spruce-peat moss forest (PICb; 70, 3.5), dry spruce-pine forest (PIN; 62, 3.7), subalpine birch forest (SB; 30, 2.7). The estimated completeness of the survey according to the Chao1 estimator was 66%, indicating that most of the more common species should have been recovered. The trend among forest associations runs mainly parallel to diversity: PICa and PICb 83%, PIN 47%, SB 57%. The myxomycete assemblage of dry coniferous forests is the most distinctive among the three forest types and shows the highest number of indicator species. The overall degree of specialization of myxomycetes is higher for substrate type than for forest associations. Among substrate types, species diversity and richness increase from litter over bark to wood.


2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Samantha Huey ◽  
Kripa Rajagopalan ◽  
Sudha Venkatramanan ◽  
Shobha Udipi ◽  
Varsha Thakker ◽  
...  

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.


2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Tao Zhou ◽  
Jiayi Chen ◽  
Yuhang Chen ◽  
Jiayi Xu ◽  
Sijing Liu ◽  
...  

Ligustrum robustum (LR) shows antiobesity effects in animal studies. However, little is known about the effect on human. The present study aimed to investigate the effect of LR intake on weight change in obese women and the role of gut microbiota. Thirty overweight and obese female participants (BMI ≥24 kg/m2) were recruited in the current study. The participants drank LR 10g/d for 12 wks. Their body composition and related biomarkers were assessed. Alterations of the gut microbiota were analyzed using 16S rRNA sequencing. The primary outcome was the change in body weight. LR intake resulted in 2.5% weight loss over 12 wks (P<0.01). Change in body fat at 12 wk was -1.77 ± 1.19 kg (P<0.01). In addition, decreased Firmicutes-to-Bacteroidetes ratio (P=0.03), increased richness (the ACE estimator, P<0.01; the Chao1 estimator, P<0.01), and altered representative taxa of the gut microbiota were observed. Bacteroidaceae, Bacteroides, Bacilli, and Lactobacillales were higher while Ruminococcaceae, Enterobacteriaceae, Enterobacteriales, Lachnospiraceae, Clostridia, and Clostridiales were lower at 12 wk. Moreover, LR intervention decreased fasting glucose (P<0.01), serum leptin (P<0.01), and IL8 (P=0.02) and increased HOMA-β (P<0.01). LR intervention moderately decreased the body weight in overweight and obese women and such effect might be due to modulation of gut microbiota.


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