scholarly journals Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

2017 ◽  
Author(s):  
Benjamin E. Rubin ◽  
Jon G. Sanders ◽  
Kyle M. Turner ◽  
Naomi E. Pierce ◽  
Sarah D. Kocher
Keyword(s):  
Social Interactions ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
De Novo ◽  
Amplicon Sequencing ◽  
Social Forms ◽  
Phylogenetic Reconstructions ◽  
16S Amplicon Sequencing ◽  
Species Specific ◽  
Genome Assemblies

AbstractSocial interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both social and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms, and most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between social and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. De novo genome assemblies indicate that these three lineages are subject to widespread relaxed selection and that Sodalis is undergoing genome degeneration during the colonization of these hosts.

scholarly journals Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

2018 ◽  
Vol 5 (7) ◽  
pp. 180369 ◽  
Author(s):  
Benjamin E. R. Rubin ◽  
Jon G. Sanders ◽  
Kyle M. Turner ◽  
Naomi E. Pierce ◽  
Sarah D. Kocher
Keyword(s):  
Social Interactions ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
Social Groups ◽  
Amplicon Sequencing ◽  
Solitary Bee ◽  
Social Forms ◽  
Phylogenetic Reconstructions ◽  
16S Amplicon Sequencing ◽  
Species Specific

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviours and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviourally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms; most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between eusocial and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. The symbiosis between halictids and Sodalis therefore appears to be in its early stages.

scholarly journals Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Michele Pittol ◽  
Erin Scully ◽  
Daniel Miller ◽  
Lisa Durso ◽  
Lidia Mariana Fiuza ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Developmental Stages ◽  
Amplicon Sequencing ◽  
Fertilizer Application ◽  
Rice Fields ◽  
Reproductive Stage ◽  
Vegetative Stage ◽  
Bacterial Phyla ◽  
16S Amplicon Sequencing ◽  
South Of Brazil

In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

scholarly journals Termites Are Associated with External Species-Specific Bacterial Communities

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Patrik Soukup ◽  
Tomáš Větrovský ◽  
Petr Stiblik ◽  
Kateřina Votýpková ◽  
Amrita Chakraborty ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Negative Effects ◽  
Termite Species ◽  
Positive Effects ◽  
Operational Taxonomic Units ◽  
Wide Range ◽  
Species Specific ◽  
And Control

ABSTRACT All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. The abundance of several bacterial OTUs, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus, was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities. IMPORTANCE As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on Rhizobiales and Actinobacteria abundance and negative effects on the abundance of several ubiquitous genera, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus. Our results demonstrate that termite galleries harbor unique bacterial communities.

scholarly journals Secondary metabolites of Bacillus subtilis impact soil-derived semi-synthetic bacterial community assembly

2020 ◽  
Author(s):  
Heiko T. Kiesewalter ◽  
Carlos N. Lozano-Andrade ◽  
Mikael L. Strube ◽  
Ákos T. Kovács
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Ecological Role ◽  
16S Amplicon Sequencing ◽  
Bacterial Protein Synthesis ◽  
Mock Communities

AbstractSecondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited.In this study, we have established soil-derived semi-synthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, its NRP deficient strain sfp or single NRP mutants incapable of producing surfactin, plipastatin or bacillaene. 16S amplicon sequencing revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundances of the two genera Lysinibacillus and Viridibacillus were reduced. Interestingly, this effect was diminished in communities supplemented with the NRPs deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicates the sensitivity of this strain towards the biosurfactant surfactin.Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semi-synthetic bacterial communities and helps to understand their ecological role.

scholarly journals Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

2020 ◽  
Vol 16 ◽  
pp. 2983-2998
Author(s):  
Heiko T Kiesewalter ◽  
Carlos N Lozano-Andrade ◽  
Mikael L Strube ◽  
Ákos T Kovács
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Ecological Role ◽  
16S Amplicon Sequencing ◽  
Bacterial Protein Synthesis ◽  
Mock Communities

Secondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular, nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition, or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established soil-derived semisynthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, the NRP-deficient strain sfp, or single-NRP mutants incapable of producing surfactin, plipastatin, or bacillaene. Through 16S amplicon sequencing, it was revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundance of the two genera Lysinibacillus and Viridibacillus was reduced. Interestingly, this effect was diminished in communities supplemented with the NRP-deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicated the sensitivity of this strain towards the biosurfactant surfactin. Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semisynthetic bacterial communities and helps to understand their ecological role.

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing

2017 ◽  
Vol 76 (2) ◽  
pp. 518-529 ◽  
Author(s):  
Kathrin Engel ◽  
Jan Sauer ◽  
Sebastian Jünemann ◽  
Anika Winkler ◽  
Daniel Wibberg ◽  
...  
Keyword(s):  
Amplicon Sequencing ◽  
16S Amplicon Sequencing ◽  
Species Specific

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

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