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

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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Study on the Diversity of Epiphytic Bacteria on Corn and Alfalfa using Illumina MiSeq/NovaSeq High-throughput Sequencing System

10.21203/rs.3.rs-561736/v1 ◽

2021 ◽

Author(s):

Mei-Xiao Wu ◽

hui Tang

Keyword(s):

High Throughput ◽

Beta Diversity ◽

High Throughput Sequencing ◽

Raw Materials ◽

Diversity Index ◽

Alpha Diversity ◽

Illumina Miseq ◽

Diversity Analysis ◽

Epiphytic Bacteria ◽

Paired End Sequencing

Abstract PurposeTo investigate the diversity of the epiphytic bacteria on corn and alfalfa collected in Hengshui city and Xingtai city, hebei province, China.MethodsIllumina MiSeq/NovaSeq High-throughput sequencing systerm was used to conduct Paired-end sequencing of community DNA fragments from surface of corn and alfalfa in Hengshui and Xingtai. QIIME2 and R language were employed to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the abundance, distribution, alpha diversity index of species, beta diversity and the differences of abundance among the samples were analyzed. ResultAt phylum level, the advantage bacterium group are Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%) and Bacteroidetes (7%). The dominant genera are Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), Hymenobacter (1%). Enterobacteriaceae (24%) are the most predominant bacteria on both corn and alfalfa samples. Alpha diversity analysis and beta diversity analysis showed that the diversity of epiphytic microbial community was significantly affected by plant species, but not by region. The diversity and richness of epiphytic bacterial community of alfalfa were significantly higher than that of corn, yet corn had more LAB than alfalfa samples. ConclusionThis study contributes to expanding our understanding of the diversity of epiphytic microorganisms in corn and alfalfa silage and provide a basis for the selection of raw materials.

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The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽

10.3390/ani11030745 ◽

2021 ◽

Vol 11 (3) ◽

pp. 745

Author(s):

Michelle Martin de Bustamante ◽

Diego Gomez ◽

Jennifer MacNicol ◽

Ralph Hamor ◽

Caryn Plummer

Keyword(s):

Beta Diversity ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Diversity Indices ◽

Rrna Gene ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Bacterial Microbiota ◽

Healthy Control ◽

Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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

Current Developments in Nutrition ◽

10.1093/cdn/nzab027 ◽

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).

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Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

Microorganisms ◽

10.3390/microorganisms9112339 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2339

Author(s):

Aleksei O. Zverev ◽

Arina A. Kichko ◽

Aleksandr G. Pinaev ◽

Nikolay A. Provorov ◽

Evgeny E. Andronov

Keyword(s):

Microbial Communities ◽

Plant Communities ◽

Plant Diversity ◽

Beta Diversity ◽

Mutual Influence ◽

Plant Root ◽

Alpha Diversity ◽

Diversity Indices ◽

Alpha And Beta Diversity ◽

Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

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

Diversity ◽

10.3390/d12030101 ◽

2020 ◽

Vol 12 (3) ◽

pp. 101 ◽

Cited By ~ 3

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.

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

Journal of Animal Science ◽

10.1093/jas/skz258.418 ◽

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.

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

10.5194/egusphere-egu21-2086 ◽

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

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 overburden soil) and sand quarry dumps followed by local undisturbed soils.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.Sand quarry dumps and regional soils looks common on phyla level, and represent common soil phyla like Proteobacteria, Actinobacteria and Verrucomicrobia. Alpha-diversity metrics aslo are similar, despite difference in beta-diversity. Overburden soil and soil from spot tips, by contrast, is very different even in phylum level. Main intermediants here are Actinobacteria, Chloroflexi &#1080; Nitrospirae. Also they show extremely low alpha-diversity metrics.This work was supported by RSF 17-16-01030, &#171;Dynamics of soil biota in chronoseries of post-technogenic landscapes: analysis of soil-ecological efficiency of ecosystem restoration processes&#187;

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Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?

BMC Pulmonary Medicine ◽

10.1186/s12890-021-01687-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Rune Nielsen ◽

Yaxin Xue ◽

Inge Jonassen ◽

Ingvild Haaland ◽

Øyvind Kommedal ◽

...

Keyword(s):

Beta Diversity ◽

Alpha Diversity ◽

Illumina Miseq ◽

Lower Airway ◽

Trend Test ◽

Rrna Gene ◽

Core Microbiome ◽

Airway Microbiome ◽

The Stability ◽

Paired End Sequencing

Abstract Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). Methods 21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS. Results A final table of 551 ASVs consisted of 19 × 106 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity. Conclusion The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.

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Ranking the Biases: The Choice of OTUs vs. ASVs in 16S rRNA Amplicon Data Analysis Has Stronger Effects On Diversity Measures Than Rarefaction and Similarity Threshold

10.21203/rs.3.rs-764430/v1 ◽

2021 ◽

Author(s):

Marlène Chiarello ◽

Mark McCauley ◽

Sébastien Villéger ◽

Colin R Jackson

Keyword(s):

16S Rrna ◽

Beta Diversity ◽

Alpha Diversity ◽

Diversity Indices ◽

Taxonomic Composition ◽

Shannon Index ◽

Minimal Impact ◽

Alpha And Beta Diversity ◽

Methodological Choices ◽

Similarity Threshold

Abstract BackgroundAdvances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from the classification and downstream analyses of traditional operational taxonomic units (OTUs), and towards the usage of amplicon sequence variants (ASVs). While ASVs have several inherent properties that make them desirable compared to OTUs, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. ResultsWe compared the respective influences of using ASVs vs. OTU-based pipelines, rarefaction of the community table, and OTU similarity threshold (97% vs. 99%) on the ecological signals detected in freshwater invertebrate and environmental (sediment, seston) 16S rRNA data sets, determining the effects on alpha diversity, beta diversity and taxonomic composition. While the choice of OTU vs. ASV pipeline significantly influenced unweighted alpha and beta diversities and changed the ecological signal detected, weighted indices such as the Shannon index, Bray-Curtis dissimilarity, and weighted Unifrac scores were not impacted by the pipeline followed. By comparison, OTU threshold and rarefaction had a minimal impact effect on all measurements, although rarefaction improved overall signals, especially in OTU-based datasets. The identification of major classes and genera identified revealed significant discrepancies across methodologies. ConclusionWe provide a list of recommendations for the analysis of 16S rRNA amplicon data. We notably recommend the use of ASVs when analyzing alpha-diversity patterns, especially in species-rich or environmental samples. Abundance weighted alpha- and beta-diversity indices should also be preferred compared to ones based on the presence-absence of biological units.

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

Journal of Animal Science ◽

10.1093/jas/skaa278.359 ◽

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.

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