scholarly journals Interrelationship between the Microbial Communities of the Root Canals and Periodontal Pockets in Combined Endodontic-Periodontal Diseases

2021 ◽  
Vol 9 (9) ◽  
pp. 1925
Author(s):  
Erica M. Lopes ◽  
Maicon R. Z. Passini ◽  
Luciano T. Kishi ◽  
Tsute Chen ◽  
Bruce J. Paster ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Periodontal Diseases ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Beta Lactam ◽  
Microbial Composition ◽  
Root Canals ◽  
Systemic Analysis ◽  
Relevant Finding

Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets (PPs) contribute to the development of endodontic-periodontal diseases. This study performed a systemic analysis using state-of-the-art sequence data to assess the microbial composition of infected RCs and PPs to further assess the microbiota and verify the possibility of cross-infection between these sites. The microbiomes of these combined diseases were examined with a focus on the V3-V4 hypervariable region of the 16S rRNA gene. The number of species in PP was higher than in RC, and there was a predominance of obligate anaerobes and gram-negative bacteria. In the RCs, the genera Enterococcus, Parvimonas, Stomatobaculum predominated, in contrast, the PPs revealed a predominance of Enterococcus, Parvimonas, Stomatobaculum, Peptostreptococcus and Mogibacterium. The RC and PP microbiome was not similar with regards to the sharing of OTUs for phyla and genera (8 and 67, respectively). The evaluation of molecular markers revealed a large number of markers for resistance to antibiotics of the carbapenem and beta-lactam type (broad spectrum). Another relevant finding of this study was the markers related to systemic diseases related to cardiac muscle and rheumatology, among others. In conclusion, the RC microbiota was less complex and diverse than PP. Interactions between microbial communities were present. The shared genus can signal communication between the endodontic and periodontal microbiomes.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows

2009 ◽  
Vol 75 (18) ◽  
pp. 5863-5870 ◽  
Author(s):  
L. Zinger ◽  
E. Coissac ◽  
P. Choler ◽  
R. A. Geremia
Keyword(s):  
Microbial Communities ◽  
Graph Partitioning ◽  
Sequence Data ◽  
Large Subunit ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Data Sets ◽  
Alignment Algorithm ◽  
Single Linkage ◽  
Phylogenetic Structure

ABSTRACT Understanding how microbial community structure and diversity respond to environmental conditions is one of the main challenges in environmental microbiology. However, there is often confusion between determining the phylogenetic structure of microbial communities and assessing the distribution and diversity of molecular operational taxonomic units (MOTUs) in these communities. This has led to the use of sequence analysis tools such as multiple alignments and hierarchical clustering that are not adapted to the analysis of large and diverse data sets and not always justified for characterization of MOTUs. Here, we developed an approach combining a pairwise alignment algorithm and graph partitioning by using MCL (Markov clustering) in order to generate discrete groups for nuclear large-subunit rRNA gene and internal transcript spacer 1 sequence data sets obtained from a yearly monitoring study of two spatially close but ecologically contrasting alpine soils (namely, early and late snowmelt locations). We compared MCL with a classical single-linkage method (Ccomps) and showed that MCL reduced bias such as the chaining effect. Using MCL, we characterized fungal communities in early and late snowmelt locations. We found contrasting distributions of MOTUs in the two soils, suggesting that there is a high level of habitat filtering in the assembly of alpine soil fungal communities. However, few MOTUs were specific to one location.

scholarly journals Distinct microbial composition and functions in an underground high-temperature hot spring at different depths

2019 ◽  
Author(s):  
Shijie Bai ◽  
Xiaotong Peng
Keyword(s):  
High Temperature ◽  
Microbial Communities ◽  
Hot Springs ◽  
Hot Spring ◽  
Hydrogen Oxidation ◽  
Archaeal Community ◽  
Limited Area ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Different Depths

Abstract. The microbial diversity and functions of three high-temperature neutral hot springs water samples at different depths (0 m, 19 m and 58 m) were investigated based on 16S rRNA gene sequencing and a functional gene array (GeoChip 5.0). The results revealed that the bacterial communities were distinct at different depths in the hot springs. Additionally, in response to the depths, bacterial/archaeal community compositions exhibited shifts over the depth profiles. Aquificae, Alpha-proteobacteria, and Deinococcus-Thermus were the dominating phyla at 0 m, 19 m, and 58 m, respectively. Hydrogenobacter, Sphingobium, and Thermus were the most abundant genera at 0 m, 19 m, and 58 m, respectively. The phylum Thaumarchaeota was the most abundant member of the archaeal community in the samples at different hot spring depths. Functional results of the microbial communities indicated that microbial metabolic functions were mainly related to sulfur, nitrogen cycling, and hydrogen oxidation. In summary, our results demonstrated that distinct microbial communities and functions were found at different depths of hot springs in a very limited area. These findings will provide new insights into the deep-subsurface biosphere associated with terrestrial hot springs.

scholarly journals Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

2021 ◽  
Vol 5 ◽  
Author(s):  
Sire Diedhiou-Sall ◽  
Komi B. Assigbetsee ◽  
Aminata N. Badiane ◽  
Ibrahima Diedhiou ◽  
M. Khouma ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Enzyme Activities ◽  
Temporal Dynamics ◽  
Dry Season ◽  
Hydraulic Lift ◽  
Annual Rainfall ◽  
Rrna Gene ◽  
28S Rrna ◽  
Microbial Composition ◽  
Row Crops

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.

scholarly journals Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Justinn Renelies-Hamilton ◽  
Kristjan Germer ◽  
David Sillam-Dussès ◽  
Kasun H. Bodawatta ◽  
Michael Poulsen
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Vertical Transmission ◽  
Priority Effects ◽  
Rrna Gene ◽  
Combined Effects ◽  
Microbial Composition ◽  
Host Fitness ◽  
Microbial Invasion ◽  
Host Taxon

ABSTRACT A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments. IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.

scholarly journals Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6199 ◽  
Author(s):  
Mark Lyte ◽  
Karrie M. Daniels ◽  
Stephan Schmitz-Esser
Keyword(s):  
Body Weight ◽  
Weight Gain ◽  
Side Effects ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Time Course ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Sequence Data ◽  
Rrna Gene ◽  
Dosing Regimen

Background Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood. Methods Male CF-1 mice (5 weeks of age, N = 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at three defined time points (0, 15 and 29 days). At the conclusion of the 29-day dosing regimen, animals were subjected to two behavioral assessments. For bacterial identification of the microbiota, 16S rRNA gene sequencing was performed on 60 fecal specimens (three specimens per mouse time course, N = 20 mice) using Illumina MiSeq. Analysis of community sequence data was done using mothur and LEfSe bioinformatic software packages. Results Daily per oral administration of fluoxetine for 29 days to male mice resulted in a significant, time dependent, alteration in microbial communities accompanying changes in body weight. The calculated species richness and diversity indicators of the murine fecal microbial communities were inconsistent and not significantly different between the groups. Among the phylotypes decreased in abundance due to fluoxetine administration were Lactobacillus johnsonii and Bacteroidales S24-7 which belong to phyla associated with regulation of body mass. The observed changes in body weight due to fluoxetine administration mimicked the dramatic shifts in weight gain/loss that has been observed in humans. Further, at the conclusion of the 29-day dosing regimen fluoxetine-dosed animals evidenced a mild anxiogenic-like behavior. Discussion We report that the most widely used antidepressant, fluoxetine, which is an SSRI-type drug, results in the selective depletion of gut microbiota, specifically the Lactobacilli which are involved in the regulation of body weight. Concomitantly, fluoxetine administration increases the abundance of phylotypes related to dysbiosis. Since Lactobacilli have been previously shown to possess a known biogenic amine transporter that regulates the uptake of fluoxetine, it is proposed that a microbial endocrinology-based mechanistic pathway is responsible for the ability of SSRIs to selectively negatively impact beneficial microbiota. The results of this study therefore suggest that the negative clinical side effects due to fluoxetine administration may be due to alterations in gut microbiota. Further, the data also suggests that supplementation of bacterial genera directly affected by fluoxetine administration may prove useful in ameliorating some of the well-known side effects of chronic fluoxetine administration such as weight alterations.

scholarly journals Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

2019 ◽  
Vol 7 (9) ◽  
pp. 357 ◽  
Author(s):  
Moonsuk Hur ◽  
Soo-Je Park
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Community Structure ◽  
16S Rrna ◽  
Microbial Communities ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Full Length ◽  
Rrna Gene ◽  
Microbial Composition

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

scholarly journals DISTINCT INTESTINAL MICROBIAL COMMUNITIES OF TWO SYMPATRIC ANADROMOUS ARCTIC SALMONIDS AND THE EFFECTS OF MIGRATION AND FEEDING

2020 ◽  
Author(s):  
Geraint Element ◽  
Katja Engel ◽  
Josh Neufeld ◽  
John Casselman ◽  
Peter Van Coeverden de Groot ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Sequence Data ◽  
Salvelinus Alpinus ◽  
Microbial Community Composition ◽  
Arctic Char ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Lake Whitefish ◽  
Abiotic And Biotic Factors

Although intestinal microbial communities from anadromous Arctic char (Salvelinus alpinus) in Kitikmeot, Nunavut, differ depending on the timing and location of capture, determinants of gut microbiota in other wild Arctic salmonids are largely unknown. Using high-throughput 16S rRNA gene sequence data, we compared intestinal microbiota from Arctic char to those from a related and sympatric salmonid, lake whitefish (Coregonus clupeaformis). Shifts in lake whitefish gut microbial community composition were observed between brackish and freshwaters, similar to impacts of salinity reported previously for Arctic char. Despite these similarities, gut community profiles for the two salmonids differed, whitefish having higher diversities and increased proportions of taxa affiliated with potential pathogens. Geography seemed to have a greater impact on freshwater whitefish gut microbiota than on corresponding Arctic char. Additionally, microbiota diversity was significantly more affected by feeding behavior in whitefish compared to sympatric Arctic char. Since sampled whitefish were at their northern range limits and grew slowly, we speculate that they, and their microbial consortia, could be more vulnerable to certain abiotic and biotic factors than Arctic char, which are well adapted to conditions found in these high latitude environments and have the most northerly distribution of any freshwater fish.

scholarly journals Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

2021 ◽  
Author(s):  
Patrick H. Thieringer ◽  
Alexander S. Honeyman ◽  
John R. Spear
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Surface Hydrology ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
High Concentrations ◽  
Recharge Rates

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular biological and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (~150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

scholarly journals Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9503
Author(s):  
Charifa Zemouri ◽  
Alexa M.G.A. Laheij ◽  
Catherine M.C. Volgenant ◽  
Bernd W. Brandt ◽  
Wim Crielaard ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Rrna Gene ◽  
Continuous Exposure ◽  
Microbial Composition ◽  
Treatment Groups ◽  
Operational Taxonomic Units ◽  
Dental Staff ◽  
Dental Unit Waterlines ◽  
Chemical Disinfectant

Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.

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