The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

The gut microbiome is affected by host intrinsic factors, diet, environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education, or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 Amplicon Sequence Variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

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Comparison of paperpoint and curette sampling of subgingival microbiome composition as analyzed by 16S rRNA gene amplicon sequencing

Journal of Oral Microbiology ◽

10.1080/20002297.2017.1325260 ◽

2017 ◽

Vol 9 (sup1) ◽

pp. 1325260

Author(s):

K. Beyer ◽

B.W. Brandt ◽

M.J. Buijs ◽

J.G. Brun ◽

W. Crielaard ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiome Composition

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Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

Microbial Ecology ◽

10.1007/s00248-021-01944-z ◽

2021 ◽

Author(s):

Artur Trzebny ◽

Anna Slodkowicz-Kowalska ◽

Johanna Björkroth ◽

Miroslawa Dabert

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Microbial Composition ◽

Microbiome Composition ◽

Microsporidian Infection ◽

Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

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Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa043 ◽

2020 ◽

Vol 96 (4) ◽

Cited By ~ 2

Author(s):

César Ruiz ◽

Marcela Villegas-Plazas ◽

Olivier P Thomas ◽

Howard Junca ◽

Thierry Pérez

Keyword(s):

Extreme Environments ◽

Amplicon Sequencing ◽

Sponge Species ◽

Rrna Gene ◽

Microbiome Composition ◽

16S Amplicon Sequencing ◽

Ecological Success ◽

Specific Community ◽

First Time ◽

The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

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rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

10.21203/rs.2.9507/v2 ◽

2019 ◽

Author(s):

Jean-Claude OGIER ◽

Sylvie Pagès ◽

Maxime Galan ◽

Matthieu Barret ◽

Sophie Gaudriault

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Taxonomic Structure ◽

Rrna Gene ◽

Specificity And Sensitivity ◽

The 16S Rrna Gene ◽

Mock Communities

Abstract Background Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3V4 hypervariable region of the 16S rRNA gene. Results We first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3V4. We applied both primers to infective juveniles of the nematode Steinernema glaseri. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium Xenorhabdus poinarii. Conclusions Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene.

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rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

10.21203/rs.2.9507/v1 ◽

2019 ◽

Author(s):

Jean-Claude OGIER ◽

Sylvie Pagès ◽

Maxime Galan ◽

Matthieu Barret ◽

Sophie Gaudriault

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Amplicon Sequencing ◽

Taxonomic Resolution ◽

Taxonomic Structure ◽

Rrna Gene ◽

Specificity And Sensitivity ◽

The 16S Rrna Gene ◽

Mock Communities

Abstract Background Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3V4 hypervariable region of the 16S rRNA gene. Results We first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3V4. We applied both primers to infective juveniles of the nematode Steinernema glaseri. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium Xenorhabdus poinarii. Conclusions Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene.

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The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

10.1101/2020.04.28.063271 ◽

2020 ◽

Author(s):

Stephanie D. Jurburg ◽

Maximilian Konzack ◽

Nico Eisenhauer ◽

Anna Heintz-Buschart

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Data Reuse ◽

Rrna Gene ◽

Data Loss ◽

Sequencing Data ◽

Data Archiving ◽

The 16S Rrna Gene ◽

Over Time

AbstractThe sequencing revolution has resulted in the explosive growth of public genetic repositories. These repositories now hold invaluable collections of 16S rRNA gene amplicon sequences, but the extent to which the currently archived data is findable, accessible, and reusable has not been evaluated. We conducted a field-wide assessment of the availability and state of publicly archived 16S rRNA gene amplicon sequencing data. Using custom-built pattern-based text extraction algorithms, we searched 26,927 publications in 17 microbiology or microbial ecology journals, and identified 2,015 studies which performed 16S rRNA gene amplicon sequencing. We found, for example, that 7.2% of these had not been made public at the time of analysis, a trend which increased over time. Of the 635 studies targeting the V3-V4 region of the 16S rRNA gene, 40.3% contained data which was not available or not reusable, and for 25.5% of the studies, faults in data formatting or data labelling were likely to create obstacles in data reuse. Taken together, only 34% of these datasets had potentially reusable data. Our study reveals significant gaps in the availability of currently deposited community sequencing data, identifies major contributors to data loss, and offers suggestions for improving data archiving practices in the future.

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Amplicon sequencing of the 16S-ITS-23S rRNA operon with long-read technology for improved phylogenetic classification of uncultured prokaryotes

10.1101/234690 ◽

2017 ◽

Cited By ~ 4

Author(s):

Joran Martijn ◽

Anders E. Lind ◽

Ian Spiers ◽

Lina Juzokaite ◽

Ignas Bunikis ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Environmental Samples ◽

Amplicon Sequencing ◽

Rrna Operon ◽

23S Rrna ◽

Rrna Gene ◽

Long Read ◽

The 16S Rrna Gene

AbstractAmplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions of environmental samples and to discover previously unknown lineages. Its unique structure of interspersed conserved and variable regions is an excellent target for PCR and allows for classification of reads at all taxonomic levels. However, the relatively few phylogenetically informative sites prevent confident phylogenetic placements of novel lineages that are deep branching relative to reference taxa. This problem is exacerbated when only short 16S rRNA gene fragments are sequenced. To resolve their placement, it is common practice to gather more informative sites by combining multiple conserved genes into concatenated datasets. This however requires genomic data which may be obtained through relatively expensive metagenome sequencing and computationally demanding analyses. Here we develop a protocol that amplifies a large part of 16S and 23S rRNA genes within the rRNA operon, including the ITS region, and sequences the amplicons with PacBio long-read technology. We tested our method with a synthetic mock community and developed a read curation pipeline that reduces the overall error rate to 0.18%. Applying our method on four diverse environmental samples, we were able to capture near full-length rRNA operon amplicons from a large diversity of prokaryotes. Phylogenetic trees constructed with these sequences showed an increase in statistical support compared to trees inferred with shorter, Illumina-like sequences using only the 16S rRNA gene (250 bp). Our method is a cost-effective solution to generate high quality, near full-length 16S and 23S rRNA gene sequences from environmental prokaryotes.

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16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary

Microbiology Resource Announcements ◽

10.1128/mra.00182-20 ◽

2020 ◽

Vol 9 (22) ◽

Author(s):

Eugenia Naro-Maciel ◽

Melissa R. Ingala ◽

Irena E. Werner ◽

Allison M. Fitzgerald

Keyword(s):

New York ◽

16S Rrna ◽

River Estuary ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequence Variants ◽

Biodiversity Monitoring ◽

South Bronx ◽

16S Rrna Amplicon Sequencing ◽

Bronx River

ABSTRACT Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 508,352 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

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16S rRNA Gene Amplicon Sequencing of Microbiota in Polybutylene Succinate Adipate-Packed Denitrification Reactors Used for Water Treatment of Land-Based Recirculating Aquaculture Systems

Microbiology Resource Announcements ◽

10.1128/mra.01295-19 ◽

2019 ◽

Vol 8 (47) ◽

Cited By ~ 2

Author(s):

Takeshi Yamada ◽

Masako Hamada ◽

Miku Nakagawa ◽

Nobukazu Sato ◽

Akinori Ando ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

High Quality ◽

Recirculating Aquaculture ◽

Recirculating Aquaculture Systems ◽

Polybutylene Succinate ◽

The 16S Rrna Gene

Information on the microbiota in polybutylene succinate adipate (PBSA)-packed denitrification reactors is limited. Here, we provide 439,817 high-quality reads of the 16S rRNA gene sequences of microbiota in PBSA-packed denitrification reactors used for land-based recirculating aquaculture. The predominant microorganisms belonged to the following families: Nocardiaceae, Chitinophagaceae, Xanthobacteraceae, Burkholderiaceae, Rhodocyclaceae, Pseudomonadaceae, Rhodanobacteraceae, and Xanthomonadaceae.

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