Microbial Community-Driven Etiopathogenesis of Peri-Implantitis

Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, and esthetic functions. Like natural teeth, the orally exposed part of dental implants offers a pristine nonshedding surface for salivary pellicle-mediated microbial adhesion and biofilm formation. In early colonization stages, these bacterial communities closely resemble those of healthy periodontal sites, with lower diversity. Because the peri-implant tissues are more susceptible to endogenous oral infections, understanding of the ecological triggers that underpin the microbial pathogenesis of peri-implantitis is central to developing improved prevention, diagnosis, and therapeutic strategies. The advent of next-generation sequencing (NGS) technologies, notably applied to 16S ribosomal RNA gene amplicons, has enabled the comprehensive taxonomic characterization of peri-implant bacterial communities in health and disease, revealing a differentially abundant microbiota between these 2 states, or with periodontitis. With that, the peri-implant niche is highlighted as a distinct ecosystem that shapes its individual resident microbial community. Shifts from health to disease include an increase in diversity and a gradual depletion of commensals, along with an enrichment of classical and emerging periodontal pathogens. Metatranscriptomic profiling revealed similarities in the virulence characteristics of microbial communities from peri-implantitis and periodontitis, nonetheless with some distinctive pathways and interbacterial networks. Deeper functional assessment of the physiology and virulence of the well-characterized microbial communities of the peri-implant niche will elucidate further the etiopathogenic mechanisms and drivers of the disease.

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Inferring directional relationships in microbial communities using signed Bayesian networks

BMC Genomics ◽

10.1186/s12864-020-07065-0 ◽

2020 ◽

Vol 21 (S6) ◽

Author(s):

Musfiqur Sazal ◽

Kalai Mathee ◽

Daniel Ruiz-Perez ◽

Trevor Cickovski ◽

Giri Narasimhan

Keyword(s):

Microbial Community ◽

Bayesian Networks ◽

Bayesian Network ◽

Microbial Communities ◽

Community Analysis ◽

Vital Role ◽

Microbe Interactions ◽

Health And Disease ◽

Colonization Patterns ◽

Host Microbe Interactions

Abstract Background Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations. Results In this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian Network (sBN). We report a surprising association between directed edges in signed BNs and known colonization orders. Conclusions BNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.

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Localization of bacterial communities within gut compartments across Cephalotes turtle ants

Applied and Environmental Microbiology ◽

10.1128/aem.02803-20 ◽

2021 ◽

Author(s):

Peter J. Flynn ◽

Catherine L. D’Amelio ◽

Jon G. Sanders ◽

Jacob A. Russell ◽

Corrie S. Moreau

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Digestive Tract ◽

Bacterial Communities ◽

Evolutionary History ◽

Amplicon Sequencing ◽

Caste Differentiation ◽

Animal Group ◽

16S Rrna Amplicon Sequencing ◽

Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

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Inferring directional relationships in microbial communities using signed Bayesian networks

10.1101/2020.02.18.955344 ◽

2020 ◽

Cited By ~ 1

Author(s):

Musfiqur Sazal ◽

Kalai Mathee ◽

Daniel Ruiz-Perez ◽

Trevor Cickovski ◽

Giri Narasimhan

Keyword(s):

Microbial Community ◽

Bayesian Networks ◽

Bayesian Network ◽

Microbial Communities ◽

Community Analysis ◽

Vital Role ◽

Microbe Interactions ◽

Health And Disease ◽

Colonization Patterns ◽

Host Microbe Interactions

AbstractBackgroundMicrobe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations.ResultsIn this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian Network (sBN). We report a surprising association between directed edges in signed BNs and known colonization orders.ConclusionsBNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.

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Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽

10.3390/d13110525 ◽

2021 ◽

Vol 13 (11) ◽

pp. 525

Author(s):

Brianna L. Boss ◽

Bianca R. Charbonneau ◽

Javier A. Izquierdo

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Environmental Gradients ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Spatial Diversity ◽

Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

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Global Comparison of the Bacterial Communities of Bilge Water, Boat Surfaces, and External Port Water

Applied and Environmental Microbiology ◽

10.1128/aem.01804-19 ◽

2019 ◽

Vol 85 (24) ◽

Cited By ~ 2

Author(s):

Laura G. Schaerer ◽

Ryan B. Ghannam ◽

Timothy M. Butler ◽

Stephen M. Techtmann

Keyword(s):

Invasive Species ◽

Microbial Community ◽

Microbial Communities ◽

Bacterial Communities ◽

Large Scale ◽

Water Discharge ◽

Global Comparison ◽

Bilge Water ◽

Significant Difference ◽

The World

ABSTRACT In the past, ballast water has been a key vector in the ship-mediated dispersal of invasive species. Here, we evaluate the potential for port microorganisms to enter and colonize the hull and bilge water of ships. Due to the small size and ubiquitous nature of bacteria, they also have the potential to be spread through hull fouling and bilge water discharge. The goal of this study was to identify the extent to which the boat microbial community is shaped by the microbial community in the port water where the boat spends most of its time. Here, we compared the microbial communities of the hull and bilge compartments of 20 boats to those of the port water in 20 different ports in five regions around the world. We found that there was a significant difference in microbial diversity between boat and port microbial communities. Despite these differences, we found that Cyanobacteria were present at high abundances in the bilge water of most vessels. Due to the limited light in the bilge, the presence of Cyanobacteria suggests that port microorganisms can enter the bilge. Using source-tracking software, we found that, on average, 40% of the bilge and 52% of the hull microbial communities were derived from water. These findings suggest that the bilge of a vessel contains a diverse microbial community that is influenced by the port microbial community and has the potential to serve as an underappreciated vector for dispersal of life. IMPORTANCE Invasive species have been a worldwide problem for many years. However, the potential for microorganisms to become invasive is relatively underexplored. As the tools to study bacterial communities become more affordable, we are able to perform large-scale studies and examine bacterial communities in higher resolution than was previously practical. This study looked at the potential for bacteria to colonize both boat surfaces and bilge water. We describe the bacterial communities on boats in 20 shipping ports in five regions around the world, describing how these microorganisms were similar to microorganisms found in port water. This suggests that the water influences the bacterial community of a boat and that microorganisms living on a boat could be moved from place to place when the boat travels.

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Organic electron donors and terminal electron acceptors structure anaerobic microbial communities and interactions in a permanently stratified sulfidic lake

10.1101/2021.02.16.431432 ◽

2021 ◽

Author(s):

Connie A. Rojas ◽

Ana De Santiago Torio ◽

Serry Park ◽

Tanja Bosak ◽

Vanja Klepac-Ceraj

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

Bacterial Communities ◽

Electron Acceptors ◽

Electron Donors ◽

Stratified Lakes ◽

Enrichment Cultures ◽

Organic Electron

AbstractThe extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (~52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin’s index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose much below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities by interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.

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Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

Online Journal of Public Health Informatics ◽

10.5210/ojphi.v7i1.5682 ◽

2015 ◽

Vol 7 (1) ◽

Author(s):

Tamar Dickerson ◽

Jonathan L. Jacobs ◽

Nicole Waybright ◽

Danielle Swales ◽

Peggy Lowary ◽

...

Keyword(s):

Next Generation Sequencing ◽

Antimicrobial Resistance ◽

Microbial Communities ◽

Bacterial Communities ◽

Temporal Dynamics ◽

Animal Health ◽

Functional Metagenomics ◽

Antimicrobial Resistance Genes ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

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The Denture-Associated Oral Microbiome in Health and Stomatitis

mSphere ◽

10.1128/msphere.00215-16 ◽

2016 ◽

Vol 1 (6) ◽

Cited By ~ 11

Author(s):

Baochen Shi ◽

Tingxi Wu ◽

Jeffrey McLean ◽

Anna Edlund ◽

Youngik Young ◽

...

Keyword(s):

Oral Health ◽

Microbial Communities ◽

Bacterial Communities ◽

Oral Microbiome ◽

Tooth Surface ◽

Inflammatory Condition ◽

Mucosal Tissue ◽

Healthy Individuals ◽

Denture Stomatitis ◽

Health And Disease

ABSTRACT Denture stomatitis is a prevalent inflammatory condition of the mucosal tissue in denture wearers that is triggered by microorganisms. While Candida has been extensively studied for its role in stomatitis etiology, the bacterial component largely remains to be investigated. Our data show that certain types of bacteria are significantly associated with denture health and disease. Furthermore, the bacterial communities residing on the teeth and dentures of the same person are similar to each other independently of the surface, and thus, denture health could impact the maintenance of remaining teeth and vice versa. While investigation of the microbiome on natural oral surfaces has generated a wealth of information, few studies have examined the microbial communities colonizing dentures and their relationship to oral health. To address this knowledge gap, we characterized the bacterial community associated with dentures and remaining teeth in healthy individuals and patients with denture stomatitis. The microbiome compositions of matched denture and tooth plaque samples of 10 healthy individuals and 9 stomatitis patients were determined by 16S rRNA gene pyrosequencing. The microbial communities colonizing dentures and remaining teeth in health and disease were very similar to each other. Matched denture and tooth samples from the same individuals shared a significantly higher percentage of identical phylotypes than random pairs of samples from different study participants. Despite these overall similarities, several bacterial phylotypes displayed discrete health- and stomatitis-associated denture colonization, while others were distinct in health and disease independently of the surface. Certain phylotypes exhibited differential colonization of dentures and teeth independently of denture health status. In conclusion, denture and natural tooth surfaces in health and stomatitis harbor similar bacterial communities. Individual-related rather than surface-specific factors play a significant role in the bacterial phylotype composition colonizing dentures and teeth. This individual-specific mutual influence on denture and tooth surface colonization could be an important factor in maintaining oral health in denture wearers. Discrete differences in colonization patterns for distinct genera and phylotypes warrant further studies regarding their potential involvement or utility as specific indicators of health and disease development in denture-wearing individuals. IMPORTANCE Denture stomatitis is a prevalent inflammatory condition of the mucosal tissue in denture wearers that is triggered by microorganisms. While Candida has been extensively studied for its role in stomatitis etiology, the bacterial component largely remains to be investigated. Our data show that certain types of bacteria are significantly associated with denture health and disease. Furthermore, the bacterial communities residing on the teeth and dentures of the same person are similar to each other independently of the surface, and thus, denture health could impact the maintenance of remaining teeth and vice versa.

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Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa132 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Xia Luo ◽

Xinyi Xiang ◽

Yuanhao Yang ◽

Guoyi Huang ◽

Kaidao Fu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Flow Rate ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Rrna Gene ◽

Strong Impact ◽

Running Waters

ABSTRACT Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance–decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.

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Deciphering Historical Water-Quality Changes Recorded in Sediments Using eDNA

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.669582 ◽

2021 ◽

Vol 9 ◽

Author(s):

Jing Sun ◽

Xueping Chen ◽

Juan Yu ◽

Zheng Chen ◽

Lihua Liu ◽

...

Keyword(s):

Water Quality ◽

Microbial Community ◽

Microbial Communities ◽

Bacterial Communities ◽

Environmental Changes ◽

Dissolved Inorganic Carbon ◽

Anthropogenic Activities ◽

Dominant Factor ◽

Overlying Water ◽

Sediment Samples

Reservoir sediments harbor abundant bacterial communities that are sensitive to substances transferred from the water column and might record historic water quality in environmental DNA (eDNA). The unique bacterial community along the sediment profile were retrieved based on eDNA in a reservoir to investigate potential links between water quality and the microbial population on a long-time scale. Bacterial communities in sediment samples gathered into three clusters along the depth (depths of 18–38, 8–18, and 1–7 cm). These three sections accumulated during three periods in which water quality was recorded in history (the pristine stage, degraded stage and remediated stage). Sediment samples from the degraded stage had lower microbial community evenness and diversity and higher microgAMBI indices than the other two sections, suggesting that poor water quality during that period was recorded in sedimental eDNA. After decades of biogeochemical cycles, statistical analysis revealed that the main factors affecting the microbial community were bromine, chlorine, and high molecular-weight PAHs in sediments from the degraded stage. The relevant functional groups Dehalococcoidia, Gemmatimonadales, Sva0485, Burkholderiales and Xanthomonadales might be indicators of the historical loading of these pollutants. Amending the microgAMBI index with our functional group of pollution can better illustrate the significant long-term environmental changes caused by historic anthropogenic activities. In sediments from the pristine stage with less pollution input, DIC (dissolved inorganic carbon) from the karst landform was the dominant factor controlling microbial communities. Whereas, the surface sediments, which accumulated during the remediated stage, had more correlation with chemistry, such as sulfate and heavy metals, in the overlying water. Our research revealed that historical changes in the water condition, that can be affected by anthropogenic activities, can be depicted by changes in the bacterial communities stored in the sediment using sedimental eDNA. Assessments of the bacterial communities in the sediments, either by describing their biodiversity or using particular species as indicators, would be potential proxies to describe historical environmental development of microbial communities.

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