scholarly journals A Meta-Analysis of the 16S-rRNA Gut Microbiome Data in Honeybees (Apis Mellifera)

2021 ◽  
Author(s):  
Alexis Gkantiragas ◽  
Jacopo Gabrielli
Keyword(s):  
Apis Mellifera ◽  
16S Rrna ◽  
Meta Analysis ◽  
Core Microbiome ◽  
Future Studies ◽  
The Core ◽  
Study Evaluation ◽  
Form Part ◽  
Microbiome Data ◽  
First Time

Honeybees (Apis Mellifera) perform an essential role in the ecosystem and economy through pollination of insect-pollinated plants, but their population is declining. Many causes of honeybees' decline are likely to be influenced by the microbiome which is thought to play an important role in bees and is particularly susceptible to infection and pesticides. However, there has been no systematic review or meta-analysis on honeybee microbiome data. Therefore, we conducted the first systematic meta-analysis of 16S-rRNA data to address this gap in the literature. Four studies were in a usable format - accounting for 336 honeybee's worth of data - the largest such dataset to the best of our knowledge. We analysed these datasets in QIIME2 and visualised the results in R-studio. For the first time, we conducted a multi-study evaluation of the core and rare bee microbiome and confirmed previous compositional microbiome data. We established that Snodgrassella, Lactobacillus, Bifidobacterium, Fructobacillus and Saccaribacter form part of the core microbiome and identify 251 rare bacterial genera. Additional components of the core microbiome were likely obscured by incomplete classification. Future studies should refine and add to our existing dataset to produce a more conclusive and high-resolution portrait of the honeybee microbiome. Furthermore, we emphasise the need for an actively curated dataset and enforcement of data sharing standards.

scholarly journals Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Héctor Argüello ◽  
Jordi Estellé ◽  
Finola C. Leonard ◽  
Fiona Crispie ◽  
Paul D. Cotter ◽  
...  
Keyword(s):  
Public Health ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Current Control ◽  
Growing Pigs ◽  
Microbiota Composition ◽  
Core Microbiome ◽  
The Core ◽  
The Impact

ABSTRACT Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.

scholarly journals Pseudomonas Can Prevent the Parasitic Fungus, While Keeping the Crop Fungus Unaffected, in the Gardens of Odontotermes Obesus.

2021 ◽  
Author(s):  
Renuka Agarwal ◽  
Manisha Gupta ◽  
Abin Antony ◽  
Ruchira Sen ◽  
Rhitoban Raychoudhury
Keyword(s):  
16S Rrna ◽  
Meta Analysis ◽  
Parasitic Fungus ◽  
Microbiota Composition ◽  
Wide Spread ◽  
The Core ◽  
Bacterial Cultures ◽  
Odontotermes Obesus ◽  
Culture Dependent

Abstract Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, takes over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the parasitic fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of Odontotermes obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the wide-spread prevalence of Pseudomonas within this termite. These evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.

scholarly journals Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets

2021 ◽  
Vol 12 ◽  
Author(s):  
Chiron J. Anderson ◽  
Lucas R. Koester ◽  
Stephan Schmitz-Esser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Species ◽  
De Novo ◽  
Management Practice ◽  
Meta Analysis ◽  
Illumina Miseq ◽  
Rumen Content ◽  
Rrna Gene ◽  
The Core

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

scholarly journals Diversity of Bacterial Biota in Capnodis tenebrionis (Coleoptera: Buprestidae) Larvae

Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 4 ◽  
Author(s):  
Hana Barak ◽  
Pradeep Kumar ◽  
Arieh Zaritsky ◽  
Zvi Mendel ◽  
Dana Ment ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Artificial Diet ◽  
Fruit Trees ◽  
Stone Fruit ◽  
The West ◽  
Future Studies ◽  
The Core ◽  
Miseq Platform ◽  
First Time

The bacterial biota in larvae of Capnodis tenebrionis, a serious pest of cultivated stone-fruit trees in the West Palearctic, was revealed for the first time using the MiSeq platform. The core bacterial community remained the same in neonates whether upon hatching or grown on peach plants or an artificial diet, suggesting that C. tenebrionis larvae acquire much of their bacterial biome from the parent adult. Reads affiliated with class levels Gammaproteobacteria and Alphaproteobacteria (phylum Proteobacteria ca. 86%), and Actinobacteria (ca. 14%) were highly abundant. Most diverse reads belong to the families Xanthomonadaceae (50%), Methylobacteriaceae (20%), Hyphomicrobiaceae (9%), Micrococcaceae (7%) and Geodermatophilaceae (4.5%). About two-thirds of the reads are affiliated with the genera Lysobacter, Microvirga, Methylobacterium, and Arthrobacter, which encompass species displaying cellulolytic and lipolytic activities. This study provides a foundation for future studies to elucidate the roles of bacterial biota in C. tenebrionis.

scholarly journals Pseudomonas can prevent the parasitic fungus, while keeping the crop fungus unaffected, in the gardens of Odontotermes obesus

2021 ◽  
Author(s):  
Renuka Agarwal ◽  
Manisha Gupta ◽  
Abin Antony ◽  
Ruchira Sen ◽  
Rhitoban Raychoudhury
Keyword(s):  
16S Rrna ◽  
Meta Analysis ◽  
Parasitic Fungus ◽  
Microbiota Composition ◽  
Wide Spread ◽  
The Core ◽  
Bacterial Cultures ◽  
Odontotermes Obesus ◽  
Culture Dependent

AbstractInsects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, takes over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the parasitic fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of Odontotermes obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the wide-spread prevalence of Pseudomonas within this termite. These evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.

scholarly journals Comprehensive exploration of the genetic contribution of the dopaminergic and serotonergic pathways to psychiatric disorders

2020 ◽  
Author(s):  
Judit Cabana-Domínguez ◽  
Bàrbara Torrico ◽  
Andreas Reif ◽  
Noèlia Fernàndez-Castillo ◽  
Bru Cormand
Keyword(s):  
Psychiatric Disorders ◽  
Meta Analysis ◽  
Genetic Contribution ◽  
Gene Set ◽  
Kegg Pathways ◽  
The Core ◽  
Gene Sets ◽  
Genetic Overlap ◽  
Gene Level ◽  
First Time

ABSTRACTPsychiatric disorders are highly prevalent and display considerable clinical and genetic overlap. Dopaminergic and serotonergic neurotransmission have been shown to have an important role in many psychiatric disorders. Here we aim to assess the genetic contribution of these systems to eight psychiatric disorders (ADHD, ANO, ASD, BIP, MD, OCD, SCZ and TS) using publicly available GWAS analyses performed by the Psychiatric Genomics Consortium. To do so, we elaborated four different gene sets using the Gene Ontology and KEGG pathways tools: two ‘wide’ selections for dopamine (DA) and for serotonin (SERT), and two ‘core’ selections for the same systems. At the gene level, we found 67 genes from the DA and/or SERT gene sets significantly associated with one of the studied disorders, and 12 of them were associated with two different disorders. Gene-set analysis revealed significant associations for ADHD and ASD with the wide DA gene set, for BIP with the wide SERT gene set, and for MD with both the core DA set and the core SERT set. Interestingly, interrogation of the cross-disorder GWAS meta-analysis displayed association with the wide DA gene set. To our knowledge, this is the first time that these two neurotransmitter systems have systematically been inspected in these disorders. Our results support a cross-disorder contribution of dopaminergic and serotonergic systems in several psychiatric conditions.

scholarly journals Periodontal and peri-implant microbiome dysbiosis is associated with alterations in the microbial community structure and local stability

2021 ◽  
Author(s):  
Yuchen Zhang ◽  
Yinhu Li ◽  
Yuguang Yang ◽  
Yiqing Wang ◽  
Xiao Cao ◽  
...  
Keyword(s):  
Community Structure ◽  
Local Stability ◽  
Oral Microbiome ◽  
Health Conditions ◽  
Metagenomic Sequencing ◽  
Core Microbiome ◽  
Future Studies ◽  
The Core ◽  
Microbial Dysbiosis ◽  
Microbial Stability

Abstract Periodontitis and peri-implantitis are common biofilm-mediated infectious diseases affecting teeth and dental implants, and have been considered to be initiated with microbial dysbiosis. To further understand the essence of oral microbiome dysbiosis in terms of bacterial interactions, community structure, and microbial stability. We analyzed 64 plaque samples from 34 participants with teeth or implants under different health conditions using metagenomic sequencing. After taxonomical annotation, we computed the core microbiome, analyzed the bacterial community structure, and calculated the microbial stability in supra- and subgingival plaques from hosts with different health conditions. The results showed that when inflammation arose, the subgingival communities became less connective and competitive with fewer hub species. In contrast, the supragingival communities tended to be more connective and competitive with an increased number of hub species. Besides, periodontitis and peri-implantitis were associated with significantly increased microbial stability in subgingival microbiome. These findings indicated that the periodontal and peri-implant dysbiosis is associated with aberrant alterations in the bacterial correlations, community structures, and local stability. The highly connected hub species, as well as the major contributing species of negative correlations should also be given more concern in future studies.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

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