scholarly journals 269 Influence of the maternal rumen microbiome on development of the calf meconium and rumen microbiome

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 195-195
Author(s):  
Kelly Woodruff ◽  
Gwendolynn Hummel ◽  
Kathleen Austin ◽  
Travis Smith ◽  
Hannah Cunningham
Keyword(s):  
Beta Diversity ◽  
Management Practices ◽  
Sequence Data ◽  
Rumen Fluid ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Sample Type ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Rumen Microbiome

Abstract Optimization of host performance may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that the cow maternal rumen microbiome would influence colonization of the calf rumen microbiome. Our objective was to relate the microbiome of the cow rumen fluid prior to parturition (RFC) and at weaning (RFCw) to the calf’s meconium microbiome (M) and calf rumen fluid microbiome at birth (RFd1), d 2 (RFd2), d 28 (RFd28), and weaning (RFNw). Multiparous Angus crossbred cows (n = 10) from the University of Wyoming beef herd were used. Rumen fluid was collected from the cows prior to parturition and at weaning. Immediately following parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again at d 2, 28, and at weaning. Microbial DNA was isolated and 16S rRNA sequencing was completed on the Illumina MiSeq. Sequence data were analyzed with QIIME2 to determine both alpha and beta diversity by sample type and day. Alpha diversity metrics reported similarities in the early gut microbiome (M, RFd1, and RFD2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition as determined by beta diversity differed in the early rumen microbiome (RFd1, RFd2, and RFd28; q ≤ 0.04). There were similarities in composition between M, RFCw, and RFd1 (q ≥ 0.09). These data can be used to develop hypotheses for the pathway of colonization in the early gut and can provide insight into management practices affecting the microbiome, improving host performance.

scholarly journals PSVI-16 Fecal microbiome of nursery pigs fed phytogenics and antibiotics

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 203-203
Author(s):  
Huyen Tran ◽  
Timothy J Johnson
Keyword(s):  
Beta Diversity ◽  
Sequence Data ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Fecal Microbiome ◽  
Nursery Pigs ◽  
Alpha And Beta Diversity ◽  
Family Level ◽  
Dietary Treatments

Abstract The objective of this study was to evaluate effects of feeding two phytogenic products (PHY1 and PHY2; blends of essential oils and plant extracts) in diets with or without antibiotics (AureoMix S 10-10; AB) on fecal microbiome of nursery pigs. A total of 400 nursery pigs (6.8 kg BW; 20 d of age) were fed one of the six dietary treatments (9 pens/treatment), including: control (0% AB; 0% phytogenics), 0.5% AB, phytogenics (0.02% PHY1 or 0.03% PHY2) or the combination of phytogenic and AB (PHY1 x AB or PHY2 x AB). On d 46 postweaning, 48 fecal samples were collected (1 pig/pen; 7–9 pigs/treatment) and were subjected to the analyses of microbial communities by using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. The sequence data were analyzed by using Qiime and the rarefied OTU table was submitted to Calypso to evaluate the alpha and beta diversity, taxonomic classification, and the differential taxa associated to the dietary treatments. There were differences among treatments on alpha diversity, where the control and PHY2 pigs had lower OTU richness (P = 0.05) and chao1 index (P < 0.10) compared to pigs fed AB alone or AB with phytogenics. There were also differences among treatments on microbial beta diversity of pigs (P < 0.01). The most abundant phyla included Firmicute, Bacteroidetes, Actinobacteria, Tenericutes, Proteobacteria, Spirochaetes, and TM7. At family level, pigs fed AB had greater Ruminococcaceae compared to the control, but lower Coriobacteriaceae and Erysipelotrichaceae compared to PHY1 or PHY2 group (P < 0.05). Feature selection by LEfSe indicated that dominant genus associated to AB treatment was Unclassified RF39, while dominant genera associated to PHY2 treatment were Cantenibacterium, unclassified Coriobacteriaceae, Blautia, Eubacterium, and Collinsella. In conclusion, feeding AB and phytogenic products had different impacts on the fecal bacteria of nursery pigs.

scholarly journals PSV-16 Influence of the late gestation maternal rumen microbiome on the calf meconium and early rumen microbiome

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 164-164
Author(s):  
Kelly Woodruff ◽  
Gwendolynn Hummel ◽  
Kathleen Austin ◽  
Travis Smith ◽  
Hannah Cunningham-Hollinger
Keyword(s):  
Beta Diversity ◽  
Rumen Fluid ◽  
Amplicon Sequencing ◽  
Late Gestation ◽  
Sample Type ◽  
Alpha And Beta Diversity ◽  
Rumen Microbiome ◽  
Beef Herd ◽  
The University ◽  
Microbial Dna

Abstract Understanding the development of the calf rumen microbiome is important in developing manipulation strategies to improve efficiency as the animal ages. We hypothesized that the cow maternal microbiome would influence the colonization of the calf rumen microbiome. Our objective was to relate the microbiomes of the cow rumen fluid (RFC) to the calf meconium (M) and calf rumen fluid (RFN) at twenty-eight days of age. Mature, multiparous Angus crossbred cows (n = 10) from the University of Wyoming beef herd were used in this study. Rumen fluid was collected from the cows prior to parturition. Immediately following parturition, meconium was collected from the calf and at 28 days post-parturition, rumen fluid was collected from the calves. Microbial DNA was isolated using a lysis buffer and mechanical bead-beating procedure and purified using the QIAamp DNA Stool Mini Kit (Qiagen). Amplicon sequencing of the 16S rRNA V4 region was completed on the MiSeq and analyzed with QIIME2. Both alpha and beta diversity were evaluated by sample type and day. Richness and evenness differed by sample type. The greatest richness and evenness was in RFC (q < 0.01) followed by RFN and M, which did not differ from each other (q ³ 0.5). Bray-Curtis and Jaccard beta diversity differed by each sample type (q < 0.01). These data indicate that the M and RFN do not differ in number and distribution of features, but the samples are compositionally different. Additionally, the RFC differed in both alpha and beta diversity from both calf samples. These profiles can be used to develop hypotheses for the pathway of colonization in the early gut yet still reflect the vast differences in the developmental stage between the cow rumen microbiome and the early calf gastrointestinal microbiome.

scholarly journals Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

2021 ◽  
Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  
Keyword(s):  
Infant Formula ◽  
Beta Diversity ◽  
Milk Fat ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Term Infants ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

scholarly journals Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 101 ◽  
Author(s):  
Sándor Bartha ◽  
Roberto Canullo ◽  
Stefano Chelli ◽  
Giandiego Campetella
Keyword(s):  
Beta Diversity ◽  
Management Practices ◽  
Multiple Scales ◽  
Forest Succession ◽  
Spatial Scales ◽  
Alpha Diversity ◽  
Structural Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Coppice Management

Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.

scholarly journals The power of microbiome studies: some considerations on which alpha and beta metrics to use and how to report analysis the results

2021 ◽  
Author(s):  
Jannigje Gerdien Kers ◽  
Edoardo Saccenti
Keyword(s):  
Sample Size ◽  
Beta Diversity ◽  
Sequence Data ◽  
Animal Experiments ◽  
Simulated Data ◽  
Alpha Diversity ◽  
Data Sets ◽  
Power Calculations ◽  
Alpha And Beta Diversity ◽  
Diversity Metrics

Abstract Since sequencing techniques become less expensive, larger sample sizes are applicable for microbiota studies. The aim of this study is to show how, and to what extent, different diversity metrics and different compositions of the microbiota influence the needed sample size to observed dissimilar groups. Empirical 16S rRNA amplicon sequence data obtained from animal experiments, observational human data, and simulated data was used to perform retrospective power calculations. A wide variation of alpha diversity and beta diversity metrics were used to compare the different microbiota data sets and the effect on the sample size. Our data showed that beta diversity metrics are most sensitive to observe differences compared to alpha diversity metrics. The structure of the data influenced which alpha metrics are most sensitive. Regarding beta diversity, the Bray-Curtis metric is in general most sensitive to observe differences between groups, resulting in lower sample size and potential publication bias. We recommend to perform power calculations and to use multiple diversity metrics as an outcome measure. To improve microbiota studies awareness needs to be raised on the sensitivity and bias for microbiota research outcomes created by the used metrics rather than biological differences. We have seen that different alpha and beta diversity metrics lead to different study power: on the basis of this observation, one could be naturally tempted to try all possible metrics until one or more are found that give a statistically significant test result, i.e. p-value < α. This way of proceeding is one of the many forms of the so-called p-value hacking. To this end, in our opinion, the only way to protect ourselves from (the temptation of) p-hacking would be to publish, and we stress here the word publish, a statistical plan before experiments are initiated: this practice is customary for clinical trials where a statistical plan describing the endpoints and the corresponding statistical analyses must be disclosed before the start of the study.

scholarly journals Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals

2021 ◽  
Vol 12 ◽  
Author(s):  
Hannah E. Epstein ◽  
Alejandra Hernandez-Agreda ◽  
Samuel Starko ◽  
Julia K. Baum ◽  
Rebecca Vega Thurber
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Beta Diversity ◽  
Sequence Data ◽  
Alpha Diversity ◽  
Gene Profiling ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
Alpha And Beta Diversity ◽  
Diversity Metrics

16S rRNA gene profiling (amplicon sequencing) is a popular technique for understanding host-associated and environmental microbial communities. Most protocols for sequencing amplicon libraries follow a standardized pipeline that can differ slightly depending on laboratory facility and user. Given that the same variable region of the 16S gene is targeted, it is generally accepted that sequencing output from differing protocols are comparable and this assumption underlies our ability to identify universal patterns in microbial dynamics through meta-analyses. However, discrepant results from a combined 16S rRNA gene dataset prepared by two labs whose protocols differed only in DNA polymerase and sequencing platform led us to scrutinize the outputs and challenge the idea of confidently combining them for standard microbiome analysis. Using technical replicates of reef-building coral samples from two species, Montipora aequituberculata and Porites lobata, we evaluated the consistency of alpha and beta diversity metrics between data resulting from these highly similar protocols. While we found minimal variation in alpha diversity between platform, significant differences were revealed with most beta diversity metrics, dependent on host species. These inconsistencies persisted following removal of low abundance taxa and when comparing across higher taxonomic levels, suggesting that bacterial community differences associated with sequencing protocol are likely to be context dependent and difficult to correct without extensive validation work. The results of this study encourage caution in the statistical comparison and interpretation of studies that combine rRNA gene sequence data from distinct protocols and point to a need for further work identifying mechanistic causes of these observed differences.

Microbiological description of self-overgrowing spoil heaps and sand quarries in Nordwest Russia

2021 ◽  
Author(s):  
Aleksei Zverev ◽  
Anastasiia Kimeklis ◽  
Grigory Gladkov ◽  
Arina Kichko ◽  
Evgeny Andronov ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Differential Abundance ◽  
Alpha And Beta Diversity ◽  
Technogenic Landscapes ◽  
Different Types ◽  
Undisturbed Soils ◽  
Disturbed Soils ◽  
Diversity Metrics

&lt;p&gt;Self-overgrowing recovery of disturbed soils is one of important processes in reclamation of disturbed soils. Different types of anthropogenic disturbances followed by variety of soil types and their genesis leads to different bacterial communities, envolved in reclamation processes. Here we describe regional self-overgrowing soils in two location (Novgorod region, Northwest Russia). We analyse top level of industrial disturbed soils after coil mining (spoil tips with extremely low pH, and &lt;span&gt;overburden &lt;/span&gt;soil) and sand quarry dumps followed by local undisturbed soils.&lt;/p&gt;&lt;p&gt;We perform 16s amplicone sequencind (v4-region) by Illumina MiSEQ and chemical routine analysis (pH, C, N and other). We provide alpha- and beta-diversity analysis, followed by CCA and analysis of differential abundance of taxa.&lt;/p&gt;&lt;p&gt;Sand quarry dumps and regional soils looks common on phyla level, and represent common soil phyla like &lt;em&gt;Proteobacteria&lt;/em&gt;, &lt;em&gt;Actinobacteria&lt;/em&gt; and &lt;em&gt;Verrucomicrobia&lt;/em&gt;. Alpha-diversity metrics aslo are similar, despite difference in beta-diversity. O&lt;span&gt;verburden soil and soil from spot tips, by contrast, is very different even in phylum level. Main intermediants here are &lt;em&gt;Actinobacteria&lt;/em&gt;, &lt;em&gt;Chloroflexi&lt;/em&gt; &amp;#1080; &lt;em&gt;Nitrospirae&lt;/em&gt;. Also they show extremely low alpha-diversity metrics.&lt;/span&gt;&lt;/p&gt;&lt;p&gt;&lt;span&gt;This work was supported by RSF 17-16-01030, &amp;#171;Dynamics of soil biota in chronoseries of post-technogenic landscapes: analysis of soil-ecological efficiency of ecosystem restoration processes&amp;#187;&lt;/span&gt;&lt;/p&gt;

scholarly journals Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1712
Author(s):  
Naren Gaowa ◽  
Kevin Panke-Buisse ◽  
Shuxiang Wang ◽  
Haibo Wang ◽  
Zhijun Cao ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Volatile Fatty Acids ◽  
Rumen Fluid ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Fatty Acid Production ◽  
Mean Pulmonary Arterial Pressure ◽  
Rumen Microbiome ◽  
Pulmonary Arterial ◽  
The Mean

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < −0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

scholarly journals Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Meixiao Wu ◽  
Yuehua Wang ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity ◽  
Paired End Sequencing

Abstract Purpose To investigate the diversity of the epiphytic bacteria on corn (Zea mays) and alfalfa (Medicago sativa) collected in Hengshui City and Xingtai City, Hebei Province, China, and explore crops suitable for natural silage. Methods The Illumina MiSeq/NovaSeq high-throughput sequencing system was used to conduct paired-end sequencing of the community DNA fragments from the surface of corn and alfalfa collected in Hengshui and Xingtai. QIIME2 and R software were used to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the alpha and beta diversity indices at of species level were calculated, and the abundance and distribution of taxa were analyzed and compared between samples. Result At phylum level, the dominant groups were Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%), and Bacteroidetes (7%). Meanwhile, the dominant genera were Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), and Hymenobacter (1%). Enterobacteriaceae (24%) were the most predominant bacteria in both the corn and alfalfa samples. Alpha diversity analysis and beta diversity indices revealed that the diversity of epiphytic microbial communities was significantly affected by plant species but not by region. The diversity and richness of the epiphytic bacterial community of alfalfa were significantly higher than those of corn. Conclusion This study contributes to the expanding knowledge on the diversity of epiphytic bacteria in corn and alfalfa silage and provides a basis for the selection of raw materials.

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