scholarly journals Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 175
Author(s):  
Li-Fang Yeo ◽  
Farhang F. Aghakhanian ◽  
James S. Y. Tan ◽  
Han Ming Gan ◽  
Maude E. Phipps
Keyword(s):  
Abdominal Obesity ◽  
Smoking Status ◽  
Age Groups ◽  
Surrogate Marker ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Peninsular Malaysia ◽  
Rrna Gene ◽  
Salting Out ◽  
High Prevalence

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium was increased in men whereas Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores, abdominal obesity and smoking status.

scholarly journals Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 175 ◽  
Author(s):  
Li-Fang Yeo ◽  
Farhang F. Aghakhanian ◽  
James S. Y. Tan ◽  
Han Ming Gan ◽  
Maude E. Phipps
Keyword(s):  
Abdominal Obesity ◽  
Smoking Status ◽  
Age Groups ◽  
Surrogate Marker ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Peninsular Malaysia ◽  
Rrna Gene ◽  
Salting Out ◽  
High Prevalence

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium, bacteria commonly found in dairy products, was increased in men. Prevotella, associated with consumption of plant-rich diets, was increased in women. Mogibacteriacea and Mycoplasma levels were significantly elevated in overweight individuals. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores and abdominal obesity and smoking status.

scholarly journals Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 175
Author(s):  
Li-Fang Yeo ◽  
Farhang F. Aghakhanian ◽  
James S. Y. Tan ◽  
Han Ming Gan ◽  
Maude E. Phipps
Keyword(s):  
Abdominal Obesity ◽  
Smoking Status ◽  
Age Groups ◽  
Surrogate Marker ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Peninsular Malaysia ◽  
Rrna Gene ◽  
Salting Out ◽  
High Prevalence

Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods:  Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R.   Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of the genus Bifidobacterium was increased in men whereas the genera Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI, abdominal obesity and smoking status.

scholarly journals Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Johanna B. Holm ◽  
Michael S. Humphrys ◽  
Courtney K. Robinson ◽  
Matthew L. Settles ◽  
Sandra Ott ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Data ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Illumina Miseq Platform ◽  
Miseq Platform

ABSTRACT Amplification, sequencing, and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and amplicon-sequencing applications have grown in the total number of samples, growth in sample multiplexing is becoming necessary while maintaining high sequence quality and sequencing depth. Here, modifications to the Illumina HiSeq 2500 platform are described which produce greater multiplexing capabilities and 300-bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-step PCR amplification protocol is also described that allows for targeting of different amplicon regions, and enhances amplification success from samples with low bacterial bioburden. IMPORTANCE Amplicon sequencing has become a popular and widespread tool for surveying microbial communities. Lower overall costs associated with high-throughput sequencing have made it a widely adopted approach, especially for projects that necessitate sample multiplexing to eliminate batch effect and reduced time to acquire data. The method for amplicon sequencing on the Illumina HiSeq 2500 platform described here provides improved multiplexing capabilities while simultaneously producing greater quality sequence data and lower per-sample cost relative to those of the Illumina MiSeq platform without sacrificing amplicon length. To make this method more flexible for various amplicon-targeted regions as well as improve amplification from low-biomass samples, we also present and validate a 2-step PCR library preparation method.

scholarly journals 246 Effect of increasing levels of dietary starch on equine cecal microbiota

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 21-21
Author(s):  
Michael Y Halpin ◽  
James Drouillard ◽  
Teresa Douthit ◽  
Qinghong Ran ◽  
Barry J Bradford ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Random Effect ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Cecal Microbiota ◽  
Dietary Starch ◽  
16 S Rrna

Abstract An experiment was conducted with 6 cecally cannulated horses (524 ± 65.5 kg BW) to evaluate effects of increasing dietary starch on equine cecal microbiota. Starch was supplied via corn pellets and was increased by 0.5 g starch/kg BW/meal every 7 d until horses received 3.5 g starch/kg BW/meal. Throughout the experiment, Smooth Bromegrass hay and water were offered ad libitum. Meals were fed every 6 h, starting at 0600 h. On d 7 of each period, cecal digesta was collected every 2 h for 12 h. Within period, cecal samples for each horse were pooled and DNA was extracted for PCR amplification of the 16 S rRNA gene (V3 and V4 regions) and sequencing via Illumina MiSeq. Alpha and beta diversity were measured. Data were analyzed as a randomized complete block with fixed effect of starch level and random effect of horse (SAS version 9.4). If a horse presented with colic, it was removed from the experiment. Parameters when feeding 1.5 g starch/kg BW/meal were compared between horses which completed the trial and those removed using covariate of 0 g starch/kg BW/meal. Feeding 1.5 g starch/kg BW/meal elicited the greatest changes in microbiota, indicated by reduced (P ≤ 0.02) operational taxonomical units and Faith phylogenetic diversity and different (P ≤ 0.017) beta diversity compared to all other treatments. Across treatments, Firmicutes was the most abundant phyla, followed by Bacteroidetes. Feeding 1.5 g starch/kg BW/meal led to lowest (P ≤ 0.0342) relative abundance (RA) of Prevotella, Treponema, Phascolarctobacterium, and [Prevotella]. Horses that persisted throughout the experiment had reduced (P = 0.0163) RA of Ruminococcus and greater RA of Phascolarctobacterium (P = 0.0057) when consuming 1.5 g starch/kg BW/meal compared to those removed. This is the first report describing effects of gradually increasing dietary starch on equine cecal microbiota in vivo.

scholarly journals Rapid Increase in the IS26-Mediated cfr Gene in E. coli Isolates with IncP and IncX4 Plasmids and Co-Existing cfr and mcr-1 Genes in a Swine Farm

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 33
Author(s):  
Zhenbao Ma ◽  
Jiao Liu ◽  
Lin Chen ◽  
Xiaoqin Liu ◽  
Wenguang Xiong ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Pulsed Field Gel Electrophoresis ◽  
Donor Strain ◽  
Swine Farm ◽  
Pulsed Field ◽  
E Coli ◽  
High Prevalence ◽  
Genetic Context

This paper aimed to investigate the molecular epidemiological features of the cfr gene in E. coli isolates in a typical swine farm during 2014–2017. A total of 617 E. coli isolates were screened for the cfr gene using PCR amplification. A susceptibility test, pulsed-field gel electrophoresis (PFGE), S1-PFGE, southern blotting hybridization, and the genetic context of the cfr gene were all used for analyzing all cfr-positive E. coli isolates. A conjugation experiment was conducted with the broth mating method using E. coli C600 as the recipient strain and 45 mcr-1-cfr-bearing E. coli isolates as the donor strain. Plasmids pHNEP124 and pHNEP129 were revealed by Illumina Miseq 2500. Eighty-five (13.7%) E. coli isolates were positive for the cfr gene and the prevalence of the cfr gene had significantly increased from 1.6% in 2014 to 29.1% in 2017. The Pulsed-Field Gel Electrophoresis (PFGE) analysis indicated that the spread of the cfr gene among E. coli isolates was mainly due to horizontal transfer. In addition, the cfr gene was primarily located on the plasmids between 28.8-kb to 60-kb in size, and the cfr gene was flanked by two copies of IS26 with the same orientation. Sequence analysis suggested that the plasmids pHNEP124 and pHNEP129 co-harboring the cfr and mcr-1 genes belonged to the plasmids IncP plasmid and IncX4 plasmid, respectively. In conclusion, this is the first study to report the high prevalence of the cfr gene among E. coli isolates and the first report of the complete genome sequence of IncP and IncX4 plasmids carrying the mcr-1 and cfr genes. The occurrence and dissemination of the cfr/mcr-1-carrying plasmids among E. coli isolates need further surveillance.

scholarly journals PSIX-16 Investigating the development of the fecal microbiome in growing diary calves

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 423-424
Author(s):  
Emily Fowler ◽  
Benoit St-Pierre
Keyword(s):  
Process Development ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Dairy Calves ◽  
Rank Test ◽  
Rrna Gene ◽  
Microbial Succession ◽  
Fecal Microbiome ◽  
Time Points

Abstract Development of the gut microbiome in young animals is critical for maximizing productivity in adults through beneficial functional contributions of symbiotic microbial communities to the health and nutrition of their host. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. A comparative analysis of the most highly represented Operational Taxonomic Units (OTU) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified both known and uncharacterized fecal bacterial species whose abundance fluctuated during development of the calves. Four highly represented OTUs were found to have a peak of abundance at week 0, which was followed by significantly lower abundance at later time points (P < 0.05). Notably, OTU JA_ 89-27339, peaked at week 0 (39.3% ± 3.6%), then declined at later time points with respective means of 2.3%, 0.1% and 0.05%. Seven other OTUs were found to peak at an intermediate time point (P < 0.05), including OTU JA_46-21334 which was found in highest abundance at week 4 (4.5% ± 1.2%) compared to means with a range of 0.001% to 0.01% for the other time points. In contrast, another set of well represented OTUs were found to increase in abundance with time, which included OTU JA_84-17601 whose abundance was highest at week 12 (1.4% ± 0.3%) (P < 0.05). These results are indicative of microbial succession in the gastrointestinal tract of dairy calves and highlight candidate bacterial species whose function could be manipulated towards improving the health and productivity of growing dairy calves.

scholarly journals Molecular detection and genetic characterization of Anaplasma marginale and Anaplasma platys-like (Rickettsiales: Anaplasmataceae) in water buffalo from eight provinces of Thailand

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Anh H. L. Nguyen ◽  
Sonthaya Tiawsirisup ◽  
Morakot Kaewthamasorn
Keyword(s):  
Water Buffalo ◽  
Pcr Amplification ◽  
Reservoir Host ◽  
Rrna Gene ◽  
Homology Searching ◽  
The Family ◽  
High Prevalence ◽  
Control And Prevention ◽  
Percentage Similarity ◽  
First Time

Abstract Background Anaplasmosis, an animal disease caused by rickettsial bacteria in the genus Anaplasma, is of considerable economic importance in livestock animals in many countries worldwide. The objectives of this study were to determine the identity, prevalence, and geographic distribution of Ehrlichia and Anaplasma in naturally infected water buffalo in Thailand using PCR amplification and sequencing of the 16S ribosomal RNA and heat shock protein groEL genes. A total of 456 buffalo blood samples from Thailand were investigated. Species identification and genetic differentiation of intra-population and inter-population with the global isolates were conducted based on nucleotide sequences. Interplay between the infection and host factors was also assessed. Results Overall, 41% of water buffalo were found to be infected with rickettsial organisms in the family Anaplasmataceae, but Ehrlichia spp., Neorickettsia spp., and Wolbachia spp. were not found in any of the sequenced samples in this study. Female buffalo were more frequently infected with bacteria in the family Anaplasmataceae than males [71 out of 176 females (40.3%) versus 11 out of 47 males (23.4%)]. The Odds Ratio value indicated that the risk of infection for female buffalo was 2.2-fold higher than that for males (p < 0.05). We detected three haplotypes of A. marginale 16S rRNA gene and they were placed in a clade that was closely related to the A. marginale in buffalo in China; and cattle in Thailand, Uganda, and China. Homology searching of groEL sequences against the GenBank™ database using the BLASTn algorithm revealed that the obtained sequences had a high percentage similarity (98.36–99.62%) to A. platys sequences. The groEL sequences of three A. platys-like isolates were clustered in the same clade as the A. platys from the tick Rhipicephalus microplus in China. Conclusions Our data showed that the apparently healthy buffalo were naturally infected by bacteria in the family Anaplasmataceae at a relatively high prevalence. We also report the finding of A. platys-like infections in water buffalo in Thailand for the first time. Water buffalo serving as the reservoir host of anaplasmosis is of concern for managing the disease control and prevention in ruminants.

scholarly journals Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Sally Ali Tawfik ◽  
Marwa Mohamed Azab ◽  
Ali Abdellah Abdelrahman Ahmed ◽  
Dalia Mukhtar Fayyad
Keyword(s):  
Pcr Amplification ◽  
Illumina Miseq ◽  
Oral Microbiome ◽  
University Hospital ◽  
Rrna Gene ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Soil Dna ◽  
Sequencing Platform ◽  
Endodontic Infections

The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level,Prevotella,Bacillus,Porphyromonas,Streptococcus, andBacteroideswere the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.

scholarly journals Sequence analysis of 12S rRNA and 16S rRNA mitochondrial genes in Iranian Afshari sheep

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Mohammad Mahmoodi ◽  
Kian Pahlevan Afshari ◽  
Hamid Reza Seyedabadi ◽  
Mehran Aboozari
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Conservation Strategies ◽  
12S Rrna ◽  
Rrna Gene ◽  
Salting Out ◽  
The Rich

Phylogenetic relationships and genetic variation in Iranian Afshari sheep breed were analyzed using 12S rRNA and 16S rRNA gene sequences. The genomic DNA was isolated by salting out method and amplified 12S rRNA and 16S rRNA genes using PCR method. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 859 and 1053 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Phylogenetic analysis of haplotype in the combination with the sheep from GenBank showed that Iranian Afshari sheep made a close to the Australian sheep cluster. This study was found informative for establishing relationships between breeds from different parts of the world. This study may facilitate the future researchers and breeders for better understanding the genetic interactions and breed differentiation for devising future breeding and conservation strategies to preserve the rich animal genetic reservoir of the country.

The Prevalence of Vitamin D Deficiency in Iran: A Literature Review

2020 ◽  
Vol 16 (7) ◽  
pp. 1015-1027
Author(s):  
Mohammad Bagherniya ◽  
Zahra Khorasanchi ◽  
Mina S. Bidokhti ◽  
Gordon A. Ferns ◽  
Mitra Rezaei ◽  
...  
Keyword(s):  
Vitamin D ◽  
Literature Review ◽  
Vitamin D Deficiency ◽  
Medical Condition ◽  
Scientific Information ◽  
Age Groups ◽  
Public Health Problem ◽  
Major Public Health Problem ◽  
Vitamin D Levels ◽  
High Prevalence

Background: Vitamin D deficiency is a common medical condition worldwide. In Iran, it has been reported that between 30-90% of people have vitamin D deficiency. However, its distribution in different parts of the country and among different age and regional groups is unclear. Therefore, the aim of this study was to review the recent literature on vitamin D deficiency in Iran. Methods: The literature review was performed using Web of Science, PubMed-Medline, Scopus and Scientific Information Database (SID) with a cut-off date of November 2016 to identify articles on vitamin D status in Iran published in the last 10 years. Studies in English and Persian that reported vitamin D levels in male and female subjects of all age groups and in healthy populations were included. Results: From 325 studies that were initially retrieved, 82 articles met the inclusion criteria. A high prevalence of vitamin D deficiency was reported, and in some regions, this was reported as >90% and was found in all age groups and in all regions of Iran. Conclusion: This review highlights the very high prevalence of vitamin D deficiency in Iran. It will be important to recognize the importance of vitamin D deficiency as a major public health problem in Iran.

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