Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome

While numerous studies implicate the microbiome in host fitness, contributions of host evolution to microbial recruitment remain largely uncharacterized. Past work has shown that plant polyploidy and domestication can influence plant biotic and abiotic interactions, yet impacts on broader microbiome assembly are still unknown for many crop species. In this study, we utilized three approaches—two field studies and one greenhouse-based experiment—to determine the degree to which patterns in bacterial community assembly in wheat (Triticum sp.) roots and rhizospheres are attributable to the host factors of ploidy level (2n, 4n, 6n) and domestication status (cultivated vs. wild). Profiling belowground bacterial communities with 16S rRNA gene amplicon sequencing, we analyzed patterns in diversity and composition. From our initial analyses of a subsetted dataset, we observed that host ploidy level was statistically significant in explaining variation in alpha and beta diversity for rhizosphere microbiomes, as well as correlated with distinct phylum-level shifts in composition, in the field. Using a reduced complexity field soil inoculum and controlled greenhouse conditions, we found some evidence suggesting that genomic lineage and ploidy level influence root alpha and beta diversity (p-value<0.05). However, in a follow-up field experiment using an expanded set of Triticum genomes that included both wild and domesticated varieties, we did not find a strong signal for either diploid genome lineages, domestication status, or ploidy level in shaping rhizosphere bacterial communities. Taken together, these results suggest that while host ploidy and domestication may have some minor influence on microbial assembly, these impacts are subtle and difficult to assess in belowground compartments for wheat varieties. By improving our understanding of the degree to which host ploidy and cultivation factors shape the plant microbiome, this research informs perspectives on what key driving forces may underlie microbiome structuring, as well as where future efforts may be best directed towards fortifying plant growth by microbial means. The greatest influence of the host on the wheat microbiome appeared to occur in the rhizosphere compartment, and we suggest that future work focuses on this environment to further characterize how host genomic and phenotypic changes influence plant-microbe communications.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

Scientific Reports ◽

10.1038/s41598-021-91387-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nadia Darwish ◽

Jonathan Shao ◽

Lori L. Schreier ◽

Monika Proszkowiec-Weglarz

Keyword(s):

16S Rrna ◽

Dna Sequences ◽

Bacterial Communities ◽

Beta Diversity ◽

Taxonomic Composition ◽

Rrna Gene ◽

Unifrac Distance ◽

Variable Regions ◽

Alpha And Beta Diversity ◽

Predicted Function

AbstractWe evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.

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Bacterial diversity along a 2 600 km river continuum

10.1101/010041 ◽

2014 ◽

Cited By ~ 1

Author(s):

Domenico Savio ◽

Lucas Sinclair ◽

Umer Z. Ijaz ◽

Philipp Stadler ◽

Alfred P. Blaschke ◽

...

Keyword(s):

Beta Diversity ◽

Amplicon Sequencing ◽

Physical Structure ◽

Danube River ◽

Rrna Gene ◽

River Continuum ◽

Alpha And Beta Diversity ◽

Continuum Concept ◽

Chemical Conditions ◽

Taxonomic Patterns

The bacterioplankton diversity in large rivers has thus far been undersampled, despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater bacteria. Based on the River Continuum Concept, we explain these taxonomic patterns and the accompanying changes in alpha and beta diversity by the physical structure and chemical conditions coupled with the hydrologic cycle along the length of the river.(version 2.1 resubmitted to Environmental Microbiology 2014-Nov-17)

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Retinitis pigmentosa is associated with shifts in the gut microbiome

Scientific Reports ◽

10.1038/s41598-021-86052-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Oksana Kutsyr ◽

Lucía Maestre-Carballa ◽

Mónica Lluesma-Gomez ◽

Manuel Martinez-Garcia ◽

Nicolás Cuenca ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Gut Microbiome ◽

Functional Decline ◽

Retinal Disease ◽

Photoreceptor Cells ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Data ◽

Alpha And Beta Diversity ◽

Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

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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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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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AB1232 ORAL DYSBIOSIS REFLECTS THE IMMUNOLOGICAL ALTERATION OF RA REGARDING TO ACPA AND HLA DRB1*SE: NAGASAKI ISLAND STUDY

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.5147 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1907.2-1907

Author(s):

Y. Tsuji ◽

M. Tamai ◽

S. Morimoto ◽

D. Sasaki ◽

M. Nagayoshi ◽

...

Keyword(s):

Beta Diversity ◽

Healthy Subjects ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Enzyme Linked Immunosorbent Assay ◽

Rrna Gene ◽

Oral Microbiota ◽

Unifrac Distance ◽

Alpha And Beta Diversity ◽

The Difference

Background:Anti-citrullinated protein antibody (ACPA) production is observed in several organs even prior to the onset of rheumatoid arthritis (RA), and oral mucosa is considered to be one of the important tissues. The presence of HLA-DRB1*SE closely associates with ACPA production. Saliva is considered to reflect the oral microbiota including periodontal disease. Alteration of oral microbiota of RA becomes to be normalized by DMARDs treatment, however, the interaction of HLA-DRB1*SE, ACPA and oral microbiota of RA patients remains to be elucidated.Objectives:The Nagasaki Island Study, which had started in 2014 collaborating with Goto City, is intended for research of the preclinical stage of RA, including ACPA/HLA genotype screening and ultrasound and magnetic resonance imaging examinations in high-risk subjects. Using the samples accumulated in this cohort, we have tried to investigate the difference of oral microbiota among RA patients and healthy subjects regarding to ACPA and HLA-DRB1*SE.Methods:Blood and salivary samples were obtained from 1422 subjects out of 4276 who have participated in the Nagasaki Island Study from 2016 to 2018. ACPA positivity was 1.7 % in total. Some of RA patients resided in Goto City participated in the Nagasaki Island Study. At this point, we selected 291 subjects, who were ACPA positive non-RA healthy subjects (n=22) and patients with RA (n=33, 11 subjects were ACPA positive and 22 ACPA negative respectively) as the case, age and gender matched ACPA negative non-RA healthy subjects (n=236) as the control. ACPA was measured by an enzyme-linked immunosorbent assay, and HLA genotyping was quantified by next-generation sequencing (Ref.1). The operational taxonomic unit (OUT) analysis using 16S rRNA gene sequencing were performed. The richness of microbial diversity within-subject (alpha diversity) was scaled via Shannon entropy. The dissimilarity between microbial community composition was calculated using Bray-Curtis distance as a scale, and differences between groups (beta diversity) were tested by permutational multivariate analysis of variance (PERMANOVA). In addition, UniFrac distance calculated in consideration of the distance on the phylogenetic tree were performed.Results:Median age 70 y.o., % Female 58.8 %. Among RA and non-RA subjects, not alpha diversity but beta diversity was statistically significance (p=0.022, small in RA). In RA subjects, both alpha and beta diversity is small (p<0.0001), especially significant in ACPA positive RA (Figure 1). Amongt RA subjects, presence of HLA-DRB1*SE did not show the difference but the tendency of being small of alpha diversity (p=0.29).Conclusion:Our study has suggested for the first time the association of oral microbiota alteration with the presence of ACPA and HLA-DRB1*SE. Oral dysbiosis may reflect the immunological status of patients with RA.References:[1]Kawaguchi S, et al. Methods Mol Biol 2018;1802: 22Disclosure of Interests:None declared

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Prospective evaluation of the fecal microbiome in dogs with large-cell lymphoma receiving chop chemotherapy

10.32469/10355/88084 ◽

2021 ◽

Author(s):

◽

Jason Couto

Keyword(s):

Microbial Diversity ◽

Beta Diversity ◽

Large Cell ◽

Amplicon Sequencing ◽

Healthy Controls ◽

Chop Chemotherapy ◽

Fecal Samples ◽

Fecal Microbiome ◽

Alpha And Beta Diversity ◽

Healthy Dogs

The fecal microbiome composition has been associated with reduced efficacy of cancer therapy and adverse side effects in humans, and chemotherapy has been shown to alter the gut microbiome. The relationship between microbiota and chemotherapy efficacy and tolerability has not been investigated in dogs. We aimed to evaluate changes in fecal microbial diversity during a cycle of CHOP chemotherapy in dogs with lymphoma and whether these changes correlated with adverse events or treatment response. Eighteen dogs with lymphoma were prospectively enrolled, and stool samples were acquired weekly for 6 weeks during CHOP. Fecal samples was analyzed via 16S rRNA amplicon sequencing as previously described. Treatment-associated differences in richness, alpha and beta diversity were determined through comparison to data from healthy controls (n = 26) using factorial ANOVA and PERMANOVA. Dogs with lymphoma had decreased fecal microbial diversity when compared with healthy controls at baseline and throughout treatment (p= 0.0002, 0.0003, 0.0001). Alpha and beta diversity did not significantly change in dogs throughout a cycle of CHOP chemotherapy (p = 0.520 and 0.995). Samples pre-treated with antibiotics were significantly less diverse (alpha and beta diversity) than untreated samples (p = 0.002, 0.0001 respectively). Dogs with lymphoma and fecal samples under the presence of antibiotics had higher levels of Escherchia species in their feces compared to normal dogs. The fecal microbiome of healthy dogs and dogs with lymphoma receiving CHOP is relatively stable over time, but dogs with lymphoma have reduced microbial diversity compared to healthy dogs before and during treatment. An increase in Proteobacteria abundance during treatment may be related to chemotherapy and/or antibiotic use.

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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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The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

Phytobiomes Journal ◽

10.1094/pbiomes-05-17-0023-r ◽

2017 ◽

Vol 1 (3) ◽

pp. 158-168 ◽

Cited By ~ 51

Author(s):

Kristi Gdanetz ◽

Frances Trail

Keyword(s):

Bacterial Communities ◽

Management Strategy ◽

Crop Yields ◽

Management Strategies ◽

Growing Season ◽

Amplicon Sequencing ◽

Antagonistic Activity ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

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