Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis

AbstractDental fluorosis is a very prevalent endemic disease. Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome. To this end, we investigated the changes in oral microbial community structure and identified bacterial species associated with moderate and severe dental fluorosis. Salivary samples of 42 individuals, assigned into Healthy (N = 9), Mild (N = 14) and Moderate/Severe (M&S, N = 19), were investigated using the V4 region of 16S rRNA gene. The oral microbial community structure based on Bray Curtis and Weighted Unifrac were significantly changed in the M&S group compared with both of Healthy and Mild. As the predominant phyla, Firmicutes and Bacteroidetes showed variation in the relative abundance among groups. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the M&S group. LEfSe analysis was used to identify differentially represented taxa at the species level. Several genera such as Streptococcus mitis, Gemella parahaemolysans, Lactococcus lactis, and Fusobacterium nucleatum, were significantly more abundant in patients with moderate/severe dental fluorosis, while Prevotella melaninogenica and Schaalia odontolytica were enriched in the Healthy group. In conclusion, our study indicates oral microbiome shift in patients with moderate/severe dental fluorosis. We identified several differentially represented bacterial species enriched in moderate and severe fluorosis. Findings from this study suggests that the roles of these bacteria in oral health and related diseases warrant more consideration in patients with moderate and severe fluorosis.

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Horizontal and Vertical Transfer of Oral Microbial Dysbiosis and Periodontal Disease

Journal of Dental Research ◽

10.1177/0022034519877150 ◽

2019 ◽

Vol 98 (13) ◽

pp. 1503-1510 ◽

Cited By ~ 7

Author(s):

M.A. Payne ◽

A. Hashim ◽

A. Alsam ◽

S. Joseph ◽

J. Aduse-Opoku ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Periodontal Disease ◽

Microbial Community Structure ◽

Bacterial Species ◽

Oral Microbiome ◽

Vertical Transfer ◽

Microbial Dysbiosis ◽

Disease Agent

One of the hallmark features of destructive periodontal disease, well documented over the last 50 y, is a change to the quantitative and qualitative composition of the associated microbiology. These alterations are now generally viewed as transformational shifts of the microbial populations associated with health leading to the emergence of bacterial species, which are only present in low abundance in health and a proportionate decrease in the abundance of others. The role of this dysbiosis of the health associated microbiota in the development of disease remains controversial: is this altered microbiology the driving agent of disease or merely a consequence of the altered environmental conditions that invariably accompany destructive disease? In this work, we aimed to address this controversy through controlled transmission experiments in the mouse in which a dysbiotic oral microbiome was transferred either horizontally or vertically into healthy recipient mice. The results of these murine studies demonstrate conclusively that natural transfer of the dysbiotic oral microbiome from a periodontally diseased individual into a healthy individual will lead to establishment of the dysbiotic community in the recipient and concomitant transmission of the disease phenotype. The inherent resilience of the dysbiotic microbial community structure in diseased animals was further demonstrated by analysis of the effects of antibiotic therapy on periodontally diseased mice. Although antibiotic treatment led to a reversal of dysbiosis of the oral microbiome, in terms of both microbial load and community structure, dysbiosis of the microbiome was reestablished following cessation of therapy. Collectively, these data suggest that an oral dysbiotic microbial community structure is stable to transfer and can act in a similar manner to a conventional transmissible infectious disease agent with concomitant effects on pathology. These findings have implications to our understanding of the role of microbial dysbiosis in the development and progression of human periodontal disease.

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Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa006 ◽

2020 ◽

Vol 96 (2) ◽

Cited By ~ 4

Author(s):

Kärt Kanger ◽

Nigel G H Guilford ◽

HyunWoo Lee ◽

Camilla L Nesbø ◽

Jaak Truu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Solid State ◽

Food Waste ◽

Microbial Community Structure ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Waste Paper ◽

Rrna Gene ◽

Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

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Effects of tobacco–peanut relay intercropping on soil bacteria community structure

Annals of Microbiology ◽

10.1007/s13213-019-01537-9 ◽

2019 ◽

Vol 69 (13) ◽

pp. 1531-1536 ◽

Cited By ~ 1

Author(s):

Lin Gao ◽

Xin-min Liu ◽

Yong-mei Du ◽

Hao Zong ◽

Guo-ming Shen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Soil Bacteria ◽

Pathogenic Bacteria ◽

Bacterial Species ◽

Continuous Cropping ◽

Soil Microbial ◽

Relay Intercropping ◽

Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

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Assessment of microbial communities in Nakivubo wetland and its catchment areas in Lake Victoria Basin, Uganda

10.1101/2020.12.08.413922 ◽

2020 ◽

Author(s):

Bernard N. Kanoi ◽

Maribet Gamboa ◽

Doris Ngonzi ◽

Thomas G. Egwang

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Diversity ◽

Microbial Community Structure ◽

Lake Victoria ◽

Rrna Gene ◽

Lake Victoria Basin ◽

Structure Changes ◽

Catchment Areas ◽

Polluted Sites

AbstractMicrobial community structure changes are key in detecting and characterizing the impacts of anthropogenic activities on aquatic ecosystems. Here, we evaluated the effect of river pollution of industrial and urban sites on the microbial community composition and distribution in the Nakivubo wetland and its catchment areas in Lake Victoria basin, Uganda. Samples were collected from two industrial and one urban polluted sites and the microbial diversity was analyzed based on a 16S rRNA gene clone library. Differences in microbial diversity and community structure were observed at different sampling points. Bacteria associated with bioremediation were found in sites receiving industrial waste, while a low proportion of important human-pathogenic bacteria were seen in urban polluted sites. While Escherichia spp. was the most dominant genus of bacteria for all sites, three unique bacteria, Bacillus sp., Pseudomonas sp., Thermomonas sp., which have been reported to transform contaminants such as heavy metals and hydrocarbons (such as oils) by their metabolic pathways were also identified. Our results may serve as a basis for further studies assessing microbial community structure changes among polluted sites at Nakivubo Water Channel for management and monitoring. The diversity of natural microbial consortia could also be a rich bioprospecting resource for novel industrial enzymes, medicinal and bioactive compounds.

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Natural Attenuation of Mn(II) in Metal Refinery Wastewater: Microbial Community Structure Analysis and Isolation of a New Mn(II)-Oxidizing Bacterium Pseudomonas sp. SK3

Water ◽

10.3390/w11030507 ◽

2019 ◽

Vol 11 (3) ◽

pp. 507 ◽

Cited By ~ 3

Author(s):

Santisak Kitjanukit ◽

Kyohei Takamatsu ◽

Naoko Okibe

Keyword(s):

Community Structure ◽

Microbial Community ◽

Structure Analysis ◽

Microbial Community Structure ◽

Natural Attenuation ◽

Rrna Gene ◽

Pseudomonas Sp ◽

Refinery Wastewater ◽

Pipe Surface

Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal refinery wastewater treatment processes.

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Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil

International Journal of Molecular Sciences ◽

10.3390/ijms20092265 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2265 ◽

Cited By ~ 9

Author(s):

Liangxiang Dai ◽

Guanchu Zhang ◽

Zipeng Yu ◽

Hong Ding ◽

Yang Xu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Drought Tolerance ◽

Microbial Communities ◽

Microbial Community Structure ◽

Defense Mechanism ◽

Developmental Stages ◽

Rrna Gene ◽

Special Importance ◽

Arachis Hypogaea L

Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

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PSIX-6 Dietary crude protein modifies fecal microbial populations independent of feed efficiency status in dairy cows

Journal of Animal Science ◽

10.1093/jas/skab235.787 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 439-440

Author(s):

Alvaro Morales ◽

Leticia Campos ◽

Jacquelyn Prestegaard ◽

Kayla Alward ◽

Connor Owens ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Feed Intake ◽

Feed Efficiency ◽

Crude Protein ◽

High Energy ◽

Repeated Measurements ◽

Rrna Gene ◽

Fecal Microbiome

Abstract Understanding the composition and structure of the fecal microbial community may provide insight into bacterial adaptation to dietary changes in cattle. The aim of this study was to determine relationships among the fecal microbiome, residual feed intake (RFI) and residual net energy intake (REI) with diets varying in crude protein (CP). Four Holstein lactating cows (806 ± 38 kg of BW) were randomly assigned to one of two treatments (LOW: 13.2% and BASE:16.6% CP) in a crossover design (2 periods of 18 d each). Cows were 260 ± 62 days in milk (DIM) and averaged 26.5 ± 12.0 kg milk yield (MY). Diets were formulated to meet animal needs. Individual feed intake measured by a Calan Gate system was used to calculate daily dry matter intake (DMI). BW, MY and milk components were also measured daily. A linear mixed model with repeated measurements over time was used to evaluate diet effect on DMI, MY, RFI and REI in SAS. Individual fecal samples were collected at the end of each period and extracted DNA was subject to 16S rRNA gene deep amplicon sequencing. Operational Taxonomic Units (OTU) were obtained using ≥97% similarity (SILVA database) and microbial community structure was assessed using alpha and beta diversity measures. No significant differences in phenotypic variables evaluated were observed between treatments or periods. We identified 927 concordant OTU among all cows, with 505 novel OTU identified in BASE cows and 403 in LOW cows. Microbial community structure was similar between treatments and feed efficiency measures. One OTU class, Erysipelotrichi, increased in abundance (P = 0.014) in BASE compared to LOW treatment. Findings reflect previous literature in which Erysipelotrichi was associated with high energy or high fat diets. Although no differences were observed in the phenotypic measurements between treatments, metagenomics analyses indicated differences in specific fecal microbial abundance.

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Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16111931 ◽

2019 ◽

Vol 16 (11) ◽

pp. 1931 ◽

Cited By ~ 3

Author(s):

Yong Li ◽

Jiejie Zhang ◽

Jianqiang Zhang ◽

Wenlai Xu ◽

Zishen Mou

Keyword(s):

Community Structure ◽

Microbial Community ◽

Total Phosphorus ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Pearson Correlation ◽

Microbial Populations ◽

Rrna Gene ◽

Overlying Water ◽

Four Seasons

To study the microbial community structure in sediments and its relation to eutrophication environment factors, the sediments and the overlying water of Sancha Lake were collected in the four seasons. MiSeq high-throughput sequencing was conducted for the V3–V4 hypervariable regions of the 16S rRNA gene and was used to analyze the microbial community structure in sediments. Pearson correlation and redundancy analysis (RDA) were conducted to determine the relation between microbial populations and eutrophic factors. The results demonstrated four main patterns: (1) in the 36 samples that were collected, the classification annotation suggested 64 phyla, 259 classes, 476 orders, 759 families, and 9325 OTUs; (2) The diversity indices were ordered according to their values as with summer > winter > autumn > spring; (3) The microbial populations in the four seasons belonged to two distinct characteristic groups; (4) pH, dissolved oxygen (DO), total phosphorus (TP), and total nitrogen (TN) had significant effects on the community composition and structure, which further affected the dissolved total phosphorus (DTP) significantly. The present study demonstrates that the microbial communities in Sancha Lake sediments are highly diverse, their compositions and distributions are significantly different between spring and non-spring, and Actinobacteria and Cyanobacteria may be the key populations or indicator organisms for eutrophication.

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Bioremediation of oil shale chemical industry solid wastes using phytoremedition and bioaugmentation

Linnaeus Eco-Tech ◽

10.15626/eco-tech.2003.007 ◽

2019 ◽

pp. 55-61

Author(s):

Jaak Truu ◽

Eeva Heinaru ◽

Ene Talpsep ◽

Eve Vedler ◽

Marti Vurmäe ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Phenolic Compounds ◽

Microbial Community Structure ◽

Oil Shale ◽

Field Experiments ◽

Bacterial Species ◽

Oil Products ◽

Rooting Depth ◽

Microbiological Methods

Although the production of oil shale energy and oil has decreased steadily during the last years with a corresponding decrease in wastes, the semi-coke mounds constitute one of the major adverse environmental challenges in Estonia The processed oil shale (semicoke) contains several organic and inorganic compounds (oil fractions, sulphides, phenolic compounds, polycyclic aromatic hydrocarbons). Laboratory and field experiments were carried out in order to test the effect of phytoremediation and bioaugmentation for remediation of pollutants in semi-coke. Four pilot test plots (50 m2 ) were established at semi-coke depository in July 2001. For bioaugmentation experiment the set of bacteria consisting of three biodegradative strains isolated from nearby area was selected. Several molecular microbiological methods were used to assess and compare the microbial community structure and diversity as well as the presence and diversity of biodegradative genes in collected samples. The dominant bacterial species based on 16S rDNA sequences in semi-coke samples were also identified. These analyses revealed that semi-coke microbial community is characterized by few dominant populations and possesses low diversity. The phytoremediation increased the number of bacteria and diversity of microbial community in semi-coke. Within a one and half year period starting from establishment of test plots, the concentration of phenolic compounds decreased up to 50% and oil products up to three times at plots with vegetation compared to control. Bioaugmentation experiment, performed in summer 2002 increased biodegradation intensity of oil products up to 50% compared to untreated planted controls. The plots, which were supplemented with laboratory-selected bacteria, were characterized by higher microbial activity and showed changes in microbial community structure. Our findings also indicate that plant growth; particularly rooting depth and belowground biomass could be enhanced by adding mixture of selected bacterial strains to semi-coke.

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Impacts of Zostera eelgrasses on microbial community structure in San Diego coastal waters

Elem Sci Anth ◽

10.1525/elementa.350 ◽

2019 ◽

Vol 7 ◽

Cited By ~ 2

Author(s):

Sahra J. Webb ◽

Tia Rabsatt ◽

Natalia Erazo ◽

Jeff S. Bowman

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

San Diego ◽

Pathogenic Bacteria ◽

Marine Ecosystem ◽

Rrna Gene ◽

Microbial Composition ◽

San Diego Bay ◽

The Impact

Marine eelgrasses are influential to their surrounding environments through their many ecosystem services, ranging from the provisioning of food and shelter for marine life to serving as a natural defense against pollution and pathogenic bacteria. In the marine waters of San Diego, CA, USA, eelgrass beds comprised of Zostera spp. are an integral part of the coastal ecosystem. To evaluate the impact of eelgrass on bacterial and archaeal community structure we collected water samples in San Diego Bay and sequenced the 16S rRNA gene from paired eelgrass-present and eelgrass-absent sites. To test the hypothesis that microbial community structure is influenced by the presence of eelgrass we applied mixed effects models to these data and to bacterial abundance data derived by flow cytometry. This approach allowed us to identify specific microbial taxa that were differentially present at eelgrass-present and eelgrass-absent sites. Principal coordinate analysis organized the samples by location (inner vs. outer bay) along the first axis, where the first two axes accounted for a 90.8% of the variance in microbial community structure among the samples. Differentially present bacterial taxa included members of the order Rickettsiales, family Flavobacteriaceae, genus Tenacibaculum and members of the order Pseudomonadales. These findings constitute a unique look into the microbial composition of San Diego Bay and examine how eelgrasses contribute to marine ecosystem health, e.g., by supporting specific microbial communities and by filtering and trapping potentially harmful bacteria to the benefit of marine organisms.

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