scholarly journals The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation

2021 ◽  
Vol 9 (10) ◽  
pp. 2011
Author(s):  
Samat Amat ◽  
Devin B. Holman ◽  
Kaycie Schmidt ◽  
Ana Clara B. Menezes ◽  
Friederike Baumgaertner ◽  
...  
Keyword(s):  
Reproductive Tract ◽  
Average Daily Gain ◽  
Methanogenic Archaea ◽  
16S Rrna Gene Sequencing ◽  
First Trimester ◽  
Vaginal Microbiota ◽  
Rrna Gene ◽  
Beef Heifers ◽  
Β Diversity ◽  
Significant Difference

In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.

scholarly journals The nasopharyngeal, ruminal, and vaginal microbiota and the core taxa shared across these microbiomes in virgin yearling heifers exposed to divergent in utero nutrition during their first trimester of gestation and in pregnant beef heifers in response to mineral supplementation

2021 ◽  
Author(s):  
Samat Amat ◽  
Devin B Holman ◽  
Kaycie Schmidt ◽  
Ana Clara B Menezes ◽  
Friederike Baumgaertner ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
First Trimester ◽  
Nervous System Development ◽  
Vaginal Microbiota ◽  
Rrna Gene ◽  
Beef Heifers ◽  
Mineral Supplement ◽  
Alpha And Beta Diversity ◽  
Significant Difference

Emerging evidence has indicated that microbial transmission from the bovine dam to her fetus may take place before birth, and that the maternal microbiota during pregnancy modulates programming of fetal metabolic and nervous system development, highlighting the potential and extended role of the maternal microbiome in calf health and development. In the present study, we characterized the nasopharyngeal, ruminal and vaginal microbiota from two cohorts of beef heifers managed at the same location: 1) virgin yearling heifers (9 months old) born from dams received gestational diets which resulted in low (LG, n = 22) or medium (MG, n = 23) weight gain during the first 84 days of gestation; and 2) pregnant replacement heifers that received a vitamin and mineral supplement (VTM, n = 17) or not (Control, n = 15) during the first 6 months of gestation. Nasopharyngeal and vaginal swabs as well as ruminal fluid were collected from both cohorts and the microbiota of each sample was assessed using 16S rRNA gene sequencing. In addition to the comparison between treatment groups within each cohort, the similarity of the microbiota of the three sample types were evaluated, and shared taxa amongst these communities were identified. The bacterial genera present in the rumen and vagina that can influence methanogenic archaeal genera were predicted using a stepwise-selected generalized linear mixed model. No significant difference was observed in the alpha and beta diversity in any of the nasopharyngeal, ruminal and vaginal microbiota between LG and MG offspring virgin heifers, or between the control and VTM pregnant heifers (p > 0.05). Subtle compositional changes in the vaginal microbiota in yearling heifers, and in the nasopharyngeal and ruminal microbiota of pregnant heifers were detected in response to treatments. Forty-one archaeal and bacterial OTUs were shared by over 60% of all samples from both virgin and pregnant heifers. Two taxa within the Methanobrevibacter genus were identified as core taxa and this genus was more relatively abundant in pregnant heifers compared to virgin heifers. Among the 25 top genera, Prevotella and Prevotella UCG-003 (negative) and Christensenellaceae R-7 group (positive) were predicted to have a significant effect on ruminal Methanobrevibacter spp. The results of this study indicate that there is little impact of divergent gestational nutrition during the first trimester on the calf microbiome at 9 months postnatal, and that VTM supplementation during pregnancy may not alter the maternal microbiome. This study provides evidence that there are several microbial taxa, including methanogenic archaea, that are shared across the respiratory, gastrointestinal, and reproductive tracts, suggesting the need for a holistic evaluation of the bovine microbiota when considering potential maternal sources for seeding calves with pioneer microbiota.

scholarly journals The Diversity of the Intestinal Flora Disturbed After Feeding Intolerance Recovery in Preterm Twins

2021 ◽  
Vol 9 ◽  
Author(s):  
Ying Li ◽  
Chunhong Jia ◽  
Xiaojun Lin ◽  
Lili Lin ◽  
Lizhen Li ◽  
...  
Keyword(s):  
Acid Metabolism ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Feeding Intolerance ◽  
Fecal Samples ◽  
Kegg Pathways ◽  
Intestinal Bacterial Community ◽  
Β Diversity ◽  
Significant Difference

Background: Feeding intolerance (FI) is a common condition in premature infants that results in growth retardation and even necrotizing enterocolitis. The gut microbiome is linked to FI occurrence; however, the outcome after FI recovery is unclear.Methods: Fecal samples were collected from 11 pairs of premature twins/triplets for 16S rRNA gene sequencing. Initial fecal samples were collected shortly after admission, and then every other week until 7 weeks or discharge.Results: After FI recovery, there was no significant difference in the β-diversity of the intestinal flora between the FI group and the feeding tolerance (FT) group. By contrast, there was a significant difference in the β-diversity. Proteobacteria was the predominant phylum in the microbiome of the FI group, whereas Firmicutes was the predominant phylum in the microbiome of the FT group. The predominant bacteria with LDA >4 between the two groups at 13–15 days after birth, 19–28 days after birth, and at discharge were different, with the proportions of Bacillus, Clostridium butyricum, and Clostridium being highest in the FT group and Firmicutes, unidentified_Clostridiales, and Proteobacteria being highest in the FI group. Similarly, there were significant differences in the relative abundances of KEGG pathways, such as fatty acid metabolism, DNA repair and recombination proteins, energy metabolism, and amino acid metabolism, between the two groups (P < 0.01).Conclusions: There was a significant difference in diversity of the intestinal flora after feeding intolerance recovery. Feeding intolerance may disturb the succession of the intestinal bacterial community.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

scholarly journals Deciphering Gut Microbiota Dysbiosis and Corresponding Genetic and Metabolic Dysregulation in Psoriasis Patients Using Metagenomics Sequencing

2021 ◽  
Vol 11 ◽  
Author(s):  
Shiju Xiao ◽  
Guangzhong Zhang ◽  
Chunyan Jiang ◽  
Xin Liu ◽  
Xiaoxu Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Target Genes ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phosphotransferase System ◽  
Microbial Composition ◽  
Kegg Pathways ◽  
Significant Difference ◽  
Rrna Gene Sequencing ◽  
Endothelial Growth Factor

BackgroundIncreasing evidence has shown that alterations in the intestinal microbiota play an important role in the pathogenesis of psoriasis. The existing relevant studies focus on 16S rRNA gene sequencing, but in-depth research on gene functions and comprehensive identification of microbiota is lacking.ObjectivesTo comprehensively identify characteristic gut microbial compositions, genetic functions and relative metabolites of patients with psoriasis and to reveal the potential pathogenesis of psoriasis.MethodsDNA was extracted from the faecal microbiota of 30 psoriatic patients and 15 healthy subjects, and metagenomics sequencing and bioinformatic analyses were performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database, cluster of orthologous groups (COG) annotations, and metabolic analyses were used to indicate relative target genes and pathways to reveal the pathogenesis of psoriasis.ResultsCompared with healthy individuals, the gut microbiota of psoriasis patients displayed an alteration in microbial taxa distribution, but no significant difference in microbial diversity. A distinct gut microbial composition in patients with psoriasis was observed, with an increased abundance of the phyla Firmicutes, Actinobacteria and Verrucomicrobia and genera Faecalibacterium, Bacteroides, Bifidobacterium, Megamonas and Roseburia and a decreased abundance of the phyla Bacteroidetes, Euryarchaeota and Proteobacteria and genera Prevotella, Alistipes, and Eubacterium. A total of 134 COGs were predicted with functional analysis, and 15 KEGG pathways, including lipopolysaccharide (LPS) biosynthesis, WNT signaling, apoptosis, bacterial secretion system, and phosphotransferase system, were significantly enriched in psoriasis patients. Five metabolites, hydrogen sulfide (H2S), isovalerate, isobutyrate, hyaluronan and hemicellulose, were significantly dysregulated in the psoriatic cohort. The dysbiosis of gut microbiota, enriched pathways and dysregulated metabolites are relevant to immune and inflammatory response, apoptosis, the vascular endothelial growth factor (VEGF) signaling pathway, gut-brain axis and brain-skin axis that play important roles in the pathogenesis of psoriasis.ConclusionsA clear dysbiosis was displayed in the gut microbiota profile, genetic functions and relative metabolites of psoriasis patients. This study is beneficial for further understanding the inflammatory pathogenesis of psoriasis and could be used to develop microbiome-based predictions and therapeutic approaches.

scholarly journals Biological Removal and Fate Assessment of Diclofenac Using Bacillus subtilis and Brevibacillus laterosporus Strains and Ecotoxicological Effects of Diclofenac and 4′-Hydroxy-diclofenac

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Camille Grandclément ◽  
Anne Piram ◽  
Marie-Eléonore Petit ◽  
Isabelle Seyssiecq ◽  
Isabelle Laffont-Schwob ◽  
...  
Keyword(s):  
Vibrio Fischeri ◽  
High Resolution Mass Spectrometry ◽  
Parent Compound ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Consortia ◽  
Brevibacillus Laterosporus ◽  
Emerging Pollutant ◽  
Significant Difference ◽  
Rrna Gene Sequencing

Since bacterial consortia involved in conventional wastewater treatment processes are not efficient in removing diclofenac (DCF), an emerging pollutant frequently detected in water bodies, the identification of microorganisms able to metabolise this pharmaceutical compound is relevant. Thus, DCF removal was investigated using bacteria isolated from aqueous stock solutions of this micropollutant and identified as Bacillus and Brevibacillus species using 16S rRNA gene sequencing. A 100% DCF removal was achieved after 17 hours of experiment at 20°C in a nutrient medium; the biodegradation kinetic followed a pseudo-first order (kbiol = 11 L·gSS−1·d−1). Quantitative assessment of DCF removal showed that its main route was biotic degradation. The main degradation product of DCF, 4′-hydroxy-diclofenac (4′-OH-DCF), was identified using liquid chromatography-electrospray ionisation high-resolution mass spectrometry. Since the ecotoxicological impact of 4′-hydroxy-diclofenac was not reported in the literature, the ecotoxicity of DCF and its metabolite were tentatively evaluated using Vibrio fischeri bioassays. Results from these tests showed that this metabolite is not more toxic than its parent compound and may hopefully be an intermediate product in the DCF transformation. Indeed, no significant difference in ecotoxicity was observed after 30 min between DCF (50 should be writtten in subscript all along the manuscript in EC50 = 23 ± 4 mg·L−1) and 4′-hydroxy-diclofenac (EC50 = 19 ± 2 mg·L−1). Besides, the study highlighted a limit of the Microtox® bioassay, which is largely used to assess ecotoxicity. The bioluminescence of Vibrio fischeri was impacted due to the production of microbial activity and the occurrence of some carbon source in the studied medium.

scholarly journals Endometrial microbiota composition is associated with reproductive outcome in infertile patients

2021 ◽  
Author(s):  
Inmaculada Moreno ◽  
Iolanda Garcia-Grau ◽  
David Perez-Villaroya ◽  
Marta Gonzalez-Monfort ◽  
Mustafa Bahçeci ◽  
...  
Keyword(s):  
Embryo Transfer ◽  
Live Birth ◽  
Reproductive Tract ◽  
Treatment Strategies ◽  
16S Rrna Gene Sequencing ◽  
Female Reproductive Tract ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Reproductive Outcome ◽  
Infertile Patients

ABSTRACTBackgroundPrevious evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage, or no pregnancy.MethodsHere we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments.ResultsA dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes.ConclusionsOur findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies.

scholarly journals Essential hypertension is associated with changes in gut microbial metabolic pathways: A multi-site analysis of ambulatory blood pressure

2021 ◽  
Author(s):  
Michael Nakai ◽  
Rosilene V Ribeiro ◽  
Bruce R. Stevens ◽  
Paul Gill ◽  
Rikeish R. Muralitharan ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Essential Hypertension ◽  
Gut Microbiota ◽  
Ambulatory Blood Pressure ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Significant Shift ◽  
Β Diversity

AbstractAimsRecent evidence supports a role for the gut microbiota in hypertension, but whether ambulatory blood pressure (BP) is associated with gut microbiota and their metabolites remains unclear. Here we characterised the function of the gut microbiota, their metabolites and receptors in untreated human hypertensive participants in metropolitan and regional areas of Australia.Methods and ResultsAmbulatory BP, faecal microbiome DNA 16S rRNA gene sequencing, plasma and faecal metabolites called short-chain fatty acid (SCFAs), and expression of their receptors were analysed in 70 untreated and otherwise healthy participants from metropolitan and regional communities. Based on machine-learning multivariate covariance analyses of de-noised amplicon sequence variant (ASV) prevalence data, we determined that there were no significant differences in gut microbiome community α- and β-diversity metrics between normotensives versus essential, white coat or masked hypertensives. However, select taxa were specific to these groups, notably Acidaminococcus spp. in essential hypertensives, and Ruminococcus spp. and Coprobacillus in normotensive subjects. Importantly, normotensive and essential hypertensive cohorts could be differentiated based on gut microbiome gene pathways and metabolites. Specifically, hypertensive participants exhibited higher plasma acetate and butyrate, but their immune cells expressed reduced levels of SCFA-activated G-protein coupled receptor 43 (GPR43).ConclusionsWhile gut microbial diversity did not change in essential hypertension, there was a significant shift in microbial gene pathways, and an increase in the circulating levels of the SCFAs acetate and butyrate. Hypertensive subjects, however, had lower levels of the SCFA-sensing receptor GPR43, putatively blunting their response to BP-lowering metabolites.

scholarly journals Effects of Giardia lamblia Colonization and Fenbendazole Treatment on Canine Fecal Microbiota

2020 ◽  
Author(s):  
Naomi N Lee ◽  
Willie A Bidot ◽  
Aaron C Ericsson ◽  
Craig L Franklin
Keyword(s):  
Giardia Lamblia ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Limited Information ◽  
Sample Collection ◽  
Minimal Impact ◽  
Clinically Normal ◽  
Significant Difference ◽  
Rrna Gene Sequencing

The gut microbiota (GM) is the sum of hundreds of distinct microbial species that can equal or outnumber their host’ssomatic cells. The GM influences a multitude of physiologic and immunologic processes in the host, and changes in the GM have been shown to alter the phenotypes of animal models. Previous studies using rodents have also shown that the composition of the GM is affected by many factors, including diet, husbandry, housing, and the genetic background of the animals. However, limited information exists about factors that may modulate GM in other laboratory species, such as dogs. We sought to eliminate sporadic Giardia colonization of dogs using fenbendazole (FBZ), an antiprotozoal widely used in biomedical research dog colonies. Concerns that FBZ could have inadvertent effects on the canine GM led us to assess GM over the course of treatment. FBZ (50 mg/kg) was given orally to all dogs in 3 different facilities (n = 19 to 25) for 10 consecutive days. Fecal samples were obtained 2 d before the initiation of treatment, on the last day of treatment, and 2 wk after the completion of treatment. Targeted 16S rRNA gene sequencing was used to analyze fecal microbiota. All dogs were clinically normal throughout the sample collection period. Statistical analyses of data showed significant differences between dogs housed in the 3 different facilities, further emphasizing the effect of housing and husbandry factors on the GM. However,negligible differences were seen between time points, indicating that FBZ did not significantly alter the canine GM. Comparison of the GM of Giardia lamblia positive and negative dogs revealed no significant difference between the 2 groups. These findings suggest that FBZ can be used therapeutically in dogs with minimal impact on the GM. Furthermore, the presence ofG. lamblia in clinically normal animals may not be sufficient to influence the normal canine microbiota.

scholarly journals Endometrial microbiota composition is associated with reproductive outcome in infertile patients

Microbiome ◽  
2022 ◽  
Vol 10 (1) ◽  
Author(s):  
Inmaculada Moreno ◽  
Iolanda Garcia-Grau ◽  
David Perez-Villaroya ◽  
Marta Gonzalez-Monfort ◽  
Mustafa Bahçeci ◽  
...  
Keyword(s):  
Embryo Transfer ◽  
Live Birth ◽  
Reproductive Tract ◽  
Treatment Strategies ◽  
16S Rrna Gene Sequencing ◽  
Female Reproductive Tract ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Reproductive Outcome ◽  
Infertile Patients

Abstract Background Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy. Methods Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments. Results A dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes. Conclusions Our findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies.

scholarly journals Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9500
Author(s):  
Xiaojuan Chen ◽  
Da He ◽  
Lianfeng Zhou ◽  
Yankun Cao ◽  
Zhanjing Li
Keyword(s):  
Algal Blooms ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Jinsha River ◽  
Kegg Pathways ◽  
Significant Difference ◽  
The Impact ◽  
Hydropower Stations

Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.

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