16s sequencing
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Author(s):  
Michael D. Thompson ◽  
Jisue Kang ◽  
Austin Faerber ◽  
Holly Hinrichs ◽  
Oguz Ozler ◽  
...  

Mice exposed in gestation to maternal high fat/high sucrose (HF/HS) diet develop altered bile acid (BA) homeostasis. We hypothesized that these reflect an altered microbiome and asked if microbiota transplanted from HF/HS offspring change hepatic BA and lipid metabolism to determine the directionality of effect. Female mice were fed HF/HS or chow (CON) for 6 weeks and bred with lean males. 16S sequencing was performed to compare taxa in offspring. Cecal microbiome transplantation (CMT) was performed from HF/HS or CON offspring into antibiotic treated mice fed chow or high fructose. BA, lipid metabolic, and gene expression analyses performed in recipient mice. Gut microbiomes from HF/HS offspring segregated from CON offspring, with increased Firmicutes to Bacteriodetes ratios and Verrucomicrobial abundance. Following CMT, HF/HS recipient mice had larger BA pools, and increased intrahepatic muricholic acid and decreased deoxycholic acid species. HF/HS recipient mice exhibited downregulated hepatic Mrp2, increased hepatic Oatp1b2, and decreased ileal Asbt mRNA expression. HF/HS recipient mice exhibited decreased cecal butyrate and increased hepatic expression of Il6. HF/HS recipient mice had larger livers, and increased intrahepatic triglyceride versus CON recipient mice after fructose feeding, with increased hepatic mRNA expression of lipogenic genes including Srebf1, Fabp1, Mogat1, and Mogat2. CMT from HF/HS offspring increased BA pool and shifted the composition of the intrahepatic BA pool. CMT from HF/HS donor offspring increased fructose-induced liver triglyceride accumulation. These findings support a causal role for vertical transfer of an altered microbiome in hepatic BA and lipid metabolism in HF/HS offspring.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Karan Goswami ◽  
Alexander J. Shope ◽  
Vasily Tokarev ◽  
Justin R. Wright ◽  
Lavinia V. Unverdorben ◽  
...  

AbstractProsthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.


2021 ◽  
Vol 12 (2) ◽  
pp. 567-573
Author(s):  
Kaiyu Pan ◽  
Lianfang Yu ◽  
Chengyue Zhang ◽  
Jianhua Zhan ◽  
Rongliang Tu

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.


2021 ◽  
Vol 9 (12) ◽  
pp. 2431
Author(s):  
Aleksandar Cojkic ◽  
Adnan Niazi ◽  
Yongzhi Guo ◽  
Triin Hallap ◽  
Peeter Padrik ◽  
...  

Reports on the use of 16S sequencing for the identification of bacteria in healthy animals are lacking. Bacterial contamination of bull semen can have a negative effect on the sperm quality. The aims of this study were threefold: to identify bacteria in the semen of healthy bulls using 16S sequencing; to investigate the differences in the bacterial community between individual bulls; and to establish if there was a relationship between the bacteria isolated and bull fertility. Semen from 18 bulls of known fertility was used for the DNA extraction and 16S sequencing; 107 bacterial genera were identified. The differences in the amplicon sequence variants (ASVs) and the numbers of genera between bulls were noted. Negative correlations (p < 0.05) between several bacterial genera with Curvibacter, Rikenellaceae RC9-gut-group and Dyella spp. were seen. Other negatively correlated bacteria were Cutibacterium, Ruminococcaceae UCG-005, Ruminococcaceae UCG-010 and Staphylococcus, all within the top 20 genera. Two genera, W5053 and Lawsonella, were enriched in bulls of low fertility; this is the first time that these bacteria have been reported in bull semen samples. The majority of the bacteria were environmental organisms or were species originating from the mucous membranes of animals and humans. The results of this study indicate that differences in the seminal microbiota of healthy bulls occur and might be correlated with fertility.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jiayuan Xie ◽  
Ming Li ◽  
Weidong Ye ◽  
Junwei Shan ◽  
Xuyang Zhao ◽  
...  

Foodborne intestinal inflammation is a major health and welfare issue in aquaculture. To prevent enteritis, various additives have been incorporated into the fish diet. Considering anti-inflammatory immune regulation, an effective natural compound could potentially treat or prevent intestinal inflammation. Our previous study has revealed galantamine’s effect on soybean induced enteritis (SBMIE) and has highlighted the possible role of the cholinergic anti-inflammatory pathway in the fish gut. To further activate the intestinal cholinergic related anti-inflammatory function, α7nAchR signaling was considered. In this study, sinomenine, a typical agonist of α7nAChR in mammals, was tested to treat fish foodborne enteritis via its potential anti-inflammation effect using the zebrafish foodborne enteritis model. After sinomenine’s dietary inclusion, results suggested that there was an alleviation of intestinal inflammation at a pathological level. This outcome was demonstrated through the improved morphology of intestinal villi. At a molecular level, SN suppressed inflammatory cytokines’ expression (especially for tnf-α) and upregulated anti-inflammation-related functions (indicated by expression of il-10, il-22, and foxp3a). To systematically understand sinomenine’s intestinal effect on SBMIE, transcriptomic analysis was done on the SBMIE adult fish model. DEGs (sinomenine vs soybean meal groups) were enriched in GO terms related to the negative regulation of lymphocyte/leukocyte activation and alpha-beta T cell proliferation, as well as the regulation of lymphocyte migration. The KEGG pathways for glycolysis and insulin signaling indicated metabolic adjustments of α7nAchR mediated anti-inflammatory effect. To demonstrate the immune cells’ response, in the SBMIE larva model, inflammatory gatherings of neutrophils, macrophages, and lymphocytes caused by soybean meal could be relieved significantly with the inclusion of sinomenine. This was consistent within the sinomenine group as CD4+ or Foxp3+ lymphocytes were found with a higher proportion at the base of mucosal folds, which may suggest the Treg population. Echoing, the sinomenine group’s 16s sequencing result, there were fewer enteritis-related TM7, Sphingomonas and Shigella, but more Cetobacterium, which were related to glucose metabolism. Our findings indicate that sinomenine hydrochloride could be important in the prevention of fish foodborne enteritis at both immune and microbiota levels.


Author(s):  
Julia V. Yudina ◽  
Alfiia I. Aminova ◽  
Andrey P. Prodeus ◽  
Anatoly A. Korsunskiy

Background. Atopic dermatitis (AD) arouses high research interest these days due to its significant morbidity rate. The most crucial risk factor for its development is the intestinal microbiota composition. The correlation of this factor with the development of AD in children requires further study. Objective. The aim of the study is to perform comparative analysis of the intestinal microbiota in 1–5 years old children with AD and conditionally healthy children via 16S-sequencing of ribosomal RNA (rRNA) of bacterial genes. Methods. We have conducted cross sectional study. 60 children with diagnosed AD and 15 conditionally healthy children aged from 1 to 5 years were surveyed. Intestinal microbiota was examined via 16S-sequencing of rRNA of bacterial genes. Results. The intestinal microbiota in children with AD and conditionally healthy children has statistically significant differences. Despite the absence of significant differences in species richness of compared groups, children with AD had the elevation in the metagenome of Proteobacteria; Bacilli and Gammaproteobacteria classes; Enterococcaceae and Veillonellaceae families; Eggerthella, Dialister and Enterobacter genus; as well as the decrease in the relative value of Actinobacteria, Bacteroidetes, Verrucomicrobia; Bacteroidales and Bifidobacteriales orders; Bifidobacteriaceae, Bacteroidaceae, Erysipelotrichaceae families; Lachnoclostridium, Roseburia, Prevotella, Coprococcus, Ruminococcus, Faecalibacterium, Bifidobacterium, Bacteroides genus; decrease of Bifidobacterium longum, Faecalibacterium prausnitzii, Bacteroides fragilis. Conclusion. It was revealed that the intestinal microbiota of children with AD has significant differences in taxonomic composition with the microbiota of conditionally healthy children. Elevation of Proteobacteria, Bacilli and Gammaproteobacteria classes, Eggerthella, Dialister and Enterobacter genus can be the risk factor for this disease development, whereas decrease of such bacteria as Verrucomicrobia, Bacteroidales and Bifidobacteriales can aggravate atopic symptoms. Thus, the need for further study of intestinal microbiota in children with AD is justified to establish the correlation of these bacteria with the disease course. 


2021 ◽  
Author(s):  
M. Senthil Kumar ◽  
Eric V. Slud ◽  
Christine Hehnly ◽  
Lijun Zhang ◽  
James Broach ◽  
...  

Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. This makes deriving health indicators based on microbiome diversity measures essential. While microbiome data generated using high throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. When this artificial inflation in the observed number of taxa (i.e., richness, a diversity measure) is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness. Here we argue that the evidence of our own experiments, theory guided exploratory data analyses and existing literature, support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed based on this finding to model a 16S survey's systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation. Such controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter. Package availability: https://github.com/mskb01/prokounter


Nutrients ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 3892
Author(s):  
Jennifer N. Martinez-Medina ◽  
Regina Flores-Lopez ◽  
Blanca E. López-Contreras ◽  
Hugo Villamil-Ramirez ◽  
Daniela Guzman-Muñoz ◽  
...  

Dietary fiber (DF) is a major substrate for the gut microbiota that contributes to metabolic health. Recent studies have shown that diet–metabolic phenotype effect might be related to individual gut microbial profiles or enterotypes. Thus, the aim of this study was to examine whether microbial enterotypes modify the association between DF intake and metabolic traits. This cross-sectional study included 204 children (6–12 years old) and 75 adults (18–60 years old). Habitual DF intake was estimated with a Food Frequency Questionnaire and biochemical, clinical and anthropometric data were obtained. Gut microbiota was assessed through 16S sequencing and participants were stratified by enterotypes. Correlations adjusting for age and sex were performed to test the associations between dietary fiber components intake and metabolic traits. In children and adults from the Prevotella enterotype, a nominal negative correlation of hemicellulose intake with insulin and HOMA-IR levels was observed (p < 0.05), while in individuals of the other enterotypes, these associations were not observed. Interestingly, the latter effect was not related to the fecal short-chain-fatty acids profile. Our results contribute to understanding the enterotype influence on the diet–phenotype interaction, which ultimate could provide evidence for their use as potential biomarkers for future precision nutrition strategies.


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