Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

Varsos, Constantinos; Patkos, Theodore; Oulas, Anastasis; Pavloudi, Christina; Gougousis, Alexandros; Ijaz, Umer Zeeshan; Filiopoulou, Irene; Pattakos, Nikolaos; Berghe, E. Vanden; Fernàndez-Guerra, Antonio; Faulwetter, Sarah; Chatzinikolaou, Eva; Pafilis, Evangelos; Bekiari, Chryssoula; Doerr, Martin; Arvanitidis, Christos

doi:10.3897/bdj.4.e8357

Cited by 15 publications

(7 citation statements)

References 9 publications

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“…Differences in turkey weights and morphometric measurements were analyzed using a one-way analysis of variance (ANOVA) with Tukey honestly significant difference (HSD) for post hoc testing. For beta diversity metrics, principal-coordinate analyses were performed in R using the vegan package (42), and differences in centroids were tested with permutational multivariate analysis of variance (PERMANOVA) (Adonis) from the vegan package, either using all groups or pairwise. Student’s t tests were used for calculating differentially abundant OTUs from CLR-transformed OTU relative abundances, as well as for calculating differences in alpha diversity metrics, weight, and normalized reactome pathway expression.…”

Section: Methodsmentioning

confidence: 99%

“…Student’s t tests were used for calculating differentially abundant OTUs from CLR-transformed OTU relative abundances, as well as for calculating differences in alpha diversity metrics, weight, and normalized reactome pathway expression. Procrustes analyses were performed in R, and significance was tested with 999 permutations and a Mantel test from the vegan package (42). Between-omic correlations were calculated using Pearson’s correlations with false-discovery rate correction of CLR-transformed abundances (bacteria and fungi) and normalized transcriptome data (microbiome package).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression

Ward

Weber

Mendoza

et al. 2019

mBio

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The microbiome is important to all animals, including poultry, playing a critical role in health and performance. Low-dose antibiotics have historically been used to modulate food production animals and their microbiome. Identifying alternatives to antibiotics conferring similar modulatory properties has been elusive. The purpose of this study was to determine if a host-tailored probiotic could recapitulate effects of a low-dose antibiotic on host response and the developing microbiome. Over 13 days of life, turkey poults were supplemented continuously with a low-dose antibiotic or oral supplementation of a prebiotic with or without two different probiotics (8 cage units, n = 80 per group). Gastrointestinal bacterial and fungal communities of poults were characterized by 16S rRNA gene and ITS2 amplicon sequencing. Localized and systemic host gene expression was assessed using transcriptome sequencing (RNA-Seq), kinase activity was assessed by avian-specific kinome peptide arrays, and performance parameters were assessed. We found that development of the early-life microbiome of turkey poults was tightly ordered in a tissue- and time-specific manner. Low-dose antibiotic and turkey-tailored probiotic supplementation, but not nontailored probiotic supplementation, elicited similar shifts in overall microbiome composition during development compared to controls. Treatment-induced bacterial changes were accompanied by parallel shifts in the fungal community and host gene expression and enhanced performance metrics. These results were validated in pen trials that identified further additive effects of the turkey-tailored probiotic combined with different prebiotics. Alternative approaches to low-dose antibiotic use in poultry are feasible and can be optimized utilizing the indigenous poultry microbiome. Similar approaches may also be beneficial for humans. IMPORTANCE Alternative approaches are greatly needed to reduce the need for antibiotic use in food animal production. This study utilized a pipeline for the development of a host-tailored probiotic to enhance performance in commercial turkeys and modulate their microbiota, similar to the effects of low-dose antibiotic administration. We determined that a host-tailored probiotic, developed in the context of the commercial turkey gut microbiome, was more effective at modulating these parameters than a nontailored probiotic cocktail. Furthermore, the host-tailored probiotic mimicked many of the effects of a low-dose antibiotic growth promoter. Surprisingly, the effects of the antibiotic growth promoter and host-tailored probiotic were observed across kingdoms, illustrating the coordinated interkingdom effects of these approaches. This work suggests that tailored approaches to probiotic development hold promise for modulating the avian host and its microbiota.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression

Ward

Weber

Mendoza

et al. 2019

mBio

View full text Add to dashboard Cite

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“…Sequence data analyses were mainly performed using QIIME and R (version 3.1.2, vegan package) [23,24]. The Abundance-based Coverage Estimator (ACE) and Shannon index were calculated based on the OTU table using QIIME.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Effects of Manure and Chemical Fertilizer on Bacterial Community Structure and Soil Enzyme Activities in North China

et al. 2021

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The application of organic fertilizer affects soil microbes and enzyme activities. In this study, we explored the effects of various long-term different fertilization treatments (manure, M; chemical fertilizer, NP; manure + chemical fertilizer, MNP; and no fertilizer, CK) on bacterial community structure and soil sucrase, urease, and alkaline phosphatase activities in Shaping, Hequ, China. High-throughput sequencing was used to amplify the third to the fourth hypervariable region of the 16S ribosomal RNA for analysis of the bacterial community structure. Enzyme activities were determined by colorimetry. Soil treated with MNP had the highest bacterial Abundance-based Coverage Estimator index and enzyme activities. The principal coordinates analysis results showed significant differences among the various fertilization treatments (p < 0.001). Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi were consistently dominant in all soil samples. The redundancy analysis and Monte Carlo permutation tests showed that the soil bacterial communities were significantly correlated with alkali-hydrolyzable nitrogen, organic matter, urease, and alkaline phosphatase. Our results reveal the fundamentally different effects that organic and inorganic fertilizers have on soil bacterial communities and their functions.

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“…The same software was used for the BIO-EN V analysis and the RELATE routine. nMDS and PERMANOVA were performed with the R virtual laboratory (RvLab) (Varsos et al 2016). Chao-1 and ACE estimator were calculated using the EstimateR function of the vegan package (Oksanen et al 2016).…”

Section: Statistical Processingmentioning

confidence: 99%

Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene

Pavloudi¹,

Oulas²,

Vasileiadou³

et al. 2017

Aquat. Microb. Ecol.

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Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase beta-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria super-cluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities

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Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)

Cited by 15 publications

References 9 publications

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression

Effects of Manure and Chemical Fertilizer on Bacterial Community Structure and Soil Enzyme Activities in North China

Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene

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