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 PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals PSIX-1 Fecal microbiome of dairy calves fed with fresh or frozen maternal colostrum or colostrum powder

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 419-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Cristiane Tomaluski ◽  
Ana Paula Silva ◽  
Sophia Dondé ◽  
Horácio Montenegro ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Illumina Miseq ◽  
Well Being ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Bacteria Growth ◽  
Miseq Platform

Abstract Besides the importance for passive immune transfer, the supply of colostrum accelerates the bacterial colonization of the calf small intestine by providing nutrients, that will function as bacteria growth substrate, as well being a microorganism inoculum source. However, it is not known whether the effect is maintained when the calves are fed with frozen colostrum or colostrum powder. The present work evaluated 15 Holstein calves housed in tropical shelters, fed one of the colostrum sources: I – fresh colostrum from the dam (n = 5), II – frozen colostrum and III – colostrum powder, a dose of 150g of IgG (n = 5). Animals fed with fresh or frozen colostrum received a corresponding volume 10% of its birth weight of high-quality colostrum (IgG > 50g / L). All animals were fed within 4h after birth. From the second meal, calves received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, calves were grouped housed, and fed with starter and coast-cross hay ad libitum. To evaluate the microbiome, fecal samples were collected at birth and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. There was no treatment effect for the diversity indices, evenness and richness. Simpson’s diversity and evenness had no effect for weeks. Weeks 1 and 2 had less Shannon’ diversity. Richness was higher for week 0. Analyzing the relative abundance, 31 phyla were identified in the fecal samples, the most abundant being Bacteriodota, Firmicutes_A, Proteobacterias, Fusobacteriota and Firmicutes. Different sources of colostrum can be used to feed dairy calves, without affecting the diversity in the colonization of the intestinal tract.

Molecular characterization and structure of intestinal micro flora for postmortem interval estimation in SD rats

2019 ◽  
Author(s):  
Huan Li ◽  
Lu Yuan ◽  
Ruina Liu ◽  
Siruo Zhang ◽  
E Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Interval Estimation ◽  
Pcr Amplification ◽  
Postmortem Interval ◽  
The Body ◽  
Rrna Gene ◽  
Variable Regions ◽  
Time Points ◽  
Almost All

Abstract Background The human rectum flora consists of a huge variety of bacteria and the association between individuals and their rectum bacterial community begins presently after birth and continues the whole lifetime. Once the body dies, the inherent microbes begin to break down from the inside and play a key role thereafter. Results The aim of this study was to investigate the probable shift of the rectum flora at different time intervals up to 15 days after death and to characterize the contribution for of this shift to estimate the time of death. The rectum of rats was wiped with a sterile cotton swab and the samples were proceeded for DNA extraction, PCR amplification of the 16S rRNA gene with the V3+V4 variable regions, and high throughput sequencing carried out on IonS5TMXL platform. The results were analyzed for intra-group and inter-group diversity, similarity and difference at different time points. At phylum level, Proteobacteria and Firmicutes showed major shifts, checked at 11 different intervals and emerged in the most of postmortem intervals. At the genus level, Enterococcus appeared in all groups except alive samples, Lactobacillus and Proteus appeared in most time points, and the latter showed an increasing trend after 3 days postmortem samples. At the species level, Enterococcus_faecalis and Proteus_mirabilis existed in most postmortem intervals, and the former had a downward trend after day 5 postmortem, while the latter had an upward trend. Corynebacterium_amycolatum , Entero_isolate_group_2 , Bacteroides_uniformis , Enterococcus_faecalis , Streptococcus_gallolyticus_subsp_macedonics , Clostridium_sporogenes were more abundant in 0-hour, day 1, 3, 5, 7, 13 postmortem intervals, respectively, while Proteus_mirabilis and Vagococcus_lutrae were abundant in day 15 postmortem. In addition, functional capacity analysis of Membrane_Transport, Amino_Acid_Metabolism, Nucleotide_Metabolism and Energy_Metabolism showed significant differences between alive and almost all other time points after death ( P <0.05). Conclusions All in all, bacteria at different levels (phylum, genera, species) showed different characteristic during the process of decomposition and possessed entirely different relative abundance and the structure of bacterial community in each time point shifted obviously, which suggested that the specific bacteria might imply the specific postmortem interval during decomposition.

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 Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262317
Author(s):  
Giovana S. Slanzon ◽  
Benjamin J. Ridenhour ◽  
Dale A. Moore ◽  
William M. Sischo ◽  
Lindsay M. Parrish ◽  
...  
Keyword(s):  
Health Status ◽  
Relative Abundance ◽  
Gastrointestinal Disease ◽  
Bifidobacterium Longum ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Probiotic Properties ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Microbiome Composition

Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4–21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli. Species of the genus Lactobacillus, such as an unclassified Lactobacillus, Lactobacillus reuteri, and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta, Bifidobacterium longum, and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E. coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.

scholarly journals Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2498
Author(s):  
Rachel Pilla ◽  
Blake C Guard ◽  
Amanda B Blake ◽  
Mark Ackermann ◽  
Craig Webb ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Elimination Diet ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Rrna Gene Sequencing ◽  
One Year ◽  
Long Term Impact

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fecal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospectively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seventy-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species were evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen metabolites were no longer different from healthy controls.

scholarly journals The Microbiology of Hemp retting in a Controlled Environment: Steering the Hemp Microbiome towards More Consistent Fiber Production

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 492 ◽  
Author(s):  
Audrey D. Law ◽  
C. Ruth McNees ◽  
Luke A. Moe
Keyword(s):  
Cannabis Sativa ◽  
Natural Fiber ◽  
Fiber Quality ◽  
Agricultural Practices ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Processing Efficiency ◽  
Fiber Production ◽  
Time Points

Industrial hemp (Cannabis sativa L.) production is increasing dramatically in the US due to recent changes which lift restrictions on the growth and sale of hemp products; however, due to the decades-long prohibition of hemp, there is a lack of current research with respect to varieties and best agricultural practices for the many uses of this versatile crop. Natural fiber production relies on retting, a microbially-mediated process necessary for the separation of fibers from the plant which can occur unevenly in the field environment and result in inconsistent fiber quality and lower processing efficiency. In this study, the microbiome of hemp stalks is investigated throughout the retting process using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform. Field retting conditions were simulated in a controlled greenhouse environment in order to determine the effects of different moisture levels and soil contact on the retting process. Samples were taken over six time points, reflecting the community of freshly cut stalks to optimally-retted material, and finally over-retted material showing degraded fibers. The results show a very consistent population throughout retting, dominated primarily by Proteobacteria, but showing an increase in the abundance of the Bacteroidetes, namely Chryseobacterium, in time points corresponding to optimally-retted and over-retted stalks in treatments receiving higher moisture levels, but not in the low-moisture treatment. Soil application did not appear to influence the microbial community throughout retting, indicating a resilient population present in and on the hemp stalks at harvest.

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 Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods

Microbiology ◽  
2004 ◽  
Vol 150 (8) ◽  
pp. 2565-2573 ◽  
Author(s):  
Xia Zhou ◽  
Stephen J. Bent ◽  
Maria G. Schneider ◽  
Catherine C. Davis ◽  
Mohammed R. Islam ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Single Species ◽  
Rrna Gene ◽  
Caucasian Women ◽  
Tract Infections

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had appreciable numbers of Megasphaera sp., Atopobium sp. and Leptotrichia sp., none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.

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.

Sign in / Sign up

Export Citation Format

Share Document