Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

ABSTRACTHost-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study found that the ground beetle microbiome is consistent across different host food sources. We used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets. Soil environment but not diet had a significant effect on bacterial diversity and composition. The three carabid species have patterns of microbial diversity similar to those previously found in other insect hosts. Metagenomic samples from two highly active tissue types — guts, and pygidial gland secretory cells (which produce defensive compounds) — were processed and sequenced separately from those of the remaining body. The observed similarity of the pygidial gland secretory cell microbiome across hosts suggests the possibility that it may be a conserved community, possibly due to functional interactions related to defensive chemistry. These results provide a baseline for future studies of the role of microbes in the diversification of defensive chemical biosynthesis in carabids.

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Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

PLoS ONE ◽

10.1371/journal.pone.0241529 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0241529

Author(s):

Anita Silver ◽

Sean Perez ◽

Melanie Gee ◽

Bethany Xu ◽

Shreeya Garg ◽

...

Keyword(s):

Microbial Diversity ◽

Ground Beetle ◽

Amplicon Sequencing ◽

Carabid Beetles ◽

Secretory Cells ◽

Pygidial Gland ◽

Defensive Compounds ◽

Highly Active ◽

16S Amplicon Sequencing ◽

Host Diet

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types—guts, and pygidial gland secretory cells (which produce defensive compounds)—were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.

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Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity

Microbial Ecology ◽

10.1007/s00248-021-01700-3 ◽

2021 ◽

Author(s):

Florian Caillon ◽

Katharina Besemer ◽

Peter Peduzzi ◽

Jakob Schelker

Keyword(s):

Microbial Diversity ◽

Bacterial Diversity ◽

Soil Water ◽

Headwater Streams ◽

High Flow ◽

Low Flow ◽

Flood Events ◽

Flow Conditions ◽

Soil Microbial ◽

Microbial Inoculation

AbstractFlood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these “dynamic pulses of microbial life” for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

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Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

10.1101/114512 ◽

2017 ◽

Cited By ~ 4

Author(s):

Jon G Sanders ◽

Piotr Lukasik ◽

Megan E Frederickson ◽

Jacob A Russell ◽

Ryuichi Koga ◽

...

Keyword(s):

16S Rrna ◽

Microbial Diversity ◽

Tropical Rainforest ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Lowland Tropical Forest ◽

16S Rrna Amplicon Sequencing ◽

Microbial Symbionts ◽

Microbial Symbiosis ◽

Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

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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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Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

Foods ◽

10.3390/foods9050622 ◽

2020 ◽

Vol 9 (5) ◽

pp. 622

Author(s):

Sabrina Saltaji ◽

Olivier Rué ◽

Valérie Sopena ◽

Sophie Sablé ◽

Fatoumata Tambadou ◽

...

Keyword(s):

Microbial Diversity ◽

Starter Culture ◽

Antimicrobial Properties ◽

Amplicon Sequencing ◽

Antimicrobial Activities ◽

Operational Taxonomic Units ◽

Soft Cheese ◽

Culture Independent ◽

Identification Of Species ◽

Species Specific

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina® (n = 5) and Pacbio® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

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A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis

Scientific Reports ◽

10.1038/s41598-020-77054-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Davide Porcellato ◽

Roger Meisal ◽

Alberto Bombelli ◽

Judith A. Narvhus

Keyword(s):

Microbial Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Lactation Period ◽

Strong Negative Correlation ◽

Udder Health ◽

Milk Samples ◽

Lactating Cows ◽

Definition Of ◽

The 16S Rrna Gene

AbstractThe importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.

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Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems

Plants ◽

10.3390/plants8110479 ◽

2019 ◽

Vol 8 (11) ◽

pp. 479 ◽

Cited By ~ 2

Author(s):

Hanif ◽

Guo ◽

Moniruzzaman ◽

He ◽

Yu ◽

...

Keyword(s):

Species Richness ◽

Microbial Diversity ◽

Soil Properties ◽

Bacterial Diversity ◽

Functional Diversity ◽

Forest Ecosystems ◽

Taxonomic Diversity ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Bacterial Richness

Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.

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Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0412 ◽

2020 ◽

Vol 66 (4) ◽

pp. 263-273

Author(s):

Julien Saavedra-Lavoie ◽

Anne de la Porte ◽

Sarah Piché-Choquette ◽

Claude Guertin ◽

Philippe Constant

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Co Oxidation ◽

Soil Microbial Communities ◽

Amplicon Sequencing ◽

Oxidative Capacity ◽

Rrna Gene ◽

Soil Microbial Diversity ◽

Soil Microcosms ◽

Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

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