scholarly journals Metagenomic Sequencing Reveals Distinct Microbial Community Structures in Healthy and Diseased Oral Microbiota

2021 ◽  
Author(s):  
Yuchen Zhang ◽  
Yinhu Li ◽  
Yuguang Yang ◽  
Yiqing Wang ◽  
Xiao Cao ◽  
...  
Keyword(s):  
Health Conditions ◽  
Oral Microbiota ◽  
Metagenomic Sequencing ◽  
Community Structures ◽  
Core Microbiome ◽  
Bacterial Interactions ◽  
The Core ◽  
Microbial Dysbiosis ◽  
Microbial Community Structures ◽  
Microbial Stability

Abstract Background: Periodontitis and peri-implantitis are common biofilm-mediated infectious diseases affecting teeth and dental implants, and have been considered to be initiated with the adjacent microbial dysbiosis. Study Aim: To further understand the essence of oral microbiota dysbiosis in terms of bacterial interactions, community structure and microbial stability.Methods: We analyzed 64 plaque samples from 34 participants with teeth or implants under different health conditions using metagenomic sequencing. After taxonomical annotation, we computed the core microbiome, analyzed the bacterial co-occurrence networks, and calculated the microbial stability in supra- and sub-gingival plaques from hosts with different health conditions. Result: When inflammation arises, the subgingival communities become less connective and competitive with fewer hub species. In contrast, the supragingival communities tend to be more connective and competitive with a increased number of hub species. Notably, periodontitis and peri-implantitis are associated with significantly increased microbial stability in subgingival plaques. In addition, we also observe similar core bacterial components yet distinct co-occurrence networks and community structures between the healthy and diseased hosts.Conclusion: The findings indicated that the aberrant changes of the bacterial co-occurrence networks and community structures are the essence of dysbiosis in periodontal and peri-implant patients, while breaking the diseased equilibrium and reestablishing healthy equilibrium is crucial for the treatment of periodontitis and peri-implantitis.

scholarly journals Periodontal and peri-implant microbiome dysbiosis is associated with alterations in the microbial community structure and local stability

2021 ◽  
Author(s):  
Yuchen Zhang ◽  
Yinhu Li ◽  
Yuguang Yang ◽  
Yiqing Wang ◽  
Xiao Cao ◽  
...  
Keyword(s):  
Community Structure ◽  
Local Stability ◽  
Oral Microbiome ◽  
Health Conditions ◽  
Metagenomic Sequencing ◽  
Core Microbiome ◽  
Future Studies ◽  
The Core ◽  
Microbial Dysbiosis ◽  
Microbial Stability

Abstract Periodontitis and peri-implantitis are common biofilm-mediated infectious diseases affecting teeth and dental implants, and have been considered to be initiated with microbial dysbiosis. To further understand the essence of oral microbiome dysbiosis in terms of bacterial interactions, community structure, and microbial stability. We analyzed 64 plaque samples from 34 participants with teeth or implants under different health conditions using metagenomic sequencing. After taxonomical annotation, we computed the core microbiome, analyzed the bacterial community structure, and calculated the microbial stability in supra- and subgingival plaques from hosts with different health conditions. The results showed that when inflammation arose, the subgingival communities became less connective and competitive with fewer hub species. In contrast, the supragingival communities tended to be more connective and competitive with an increased number of hub species. Besides, periodontitis and peri-implantitis were associated with significantly increased microbial stability in subgingival microbiome. These findings indicated that the periodontal and peri-implant dysbiosis is associated with aberrant alterations in the bacterial correlations, community structures, and local stability. The highly connected hub species, as well as the major contributing species of negative correlations should also be given more concern in future studies.

scholarly journals Core of the saliva microbiome: an analysis of the MG-RAST data

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Simone G. Oliveira ◽  
Rafaela R. Nishiyama ◽  
Claudio A. C. Trigo ◽  
Ana Luiza Mattos-Guaraldi ◽  
Alberto M. R. Dávila ◽  
...  
Keyword(s):  
Statistical Tests ◽  
Principal Component ◽  
Amplicon Sequencing ◽  
Health Condition ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Core Microbiome ◽  
Shotgun Metagenomics ◽  
The Core ◽  
Spearman’S Correlation

Abstract Background Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms. Methods Projects containing the term “SALIVA”, deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann–Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used. Results The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r =  − 0.78) and the lowest between Alpha and Unknown (r =  − 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r =  − 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter. Conclusions Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

scholarly journals Oral microbial dysbiosis and its performance in predicting oral cancer

2020 ◽  
Author(s):  
Shih-Chi Su ◽  
Lun-Ching Chang ◽  
Hsien-Da Huang ◽  
Chih-Yu Peng ◽  
Chun-Yi Chuang ◽  
...  
Keyword(s):  
Oral Cancer ◽  
Fusobacterium Nucleatum ◽  
Risky Behaviors ◽  
Health Condition ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Microbial Dysbiosis ◽  
Anti Cancer ◽  
Betel Quid Chewing ◽  
Male Patients

Abstract Dysbiosis of oral microbiome may dictate the progression of oral squamous cell carcinoma (OSCC). Yet, the composition of oral microbiome fluctuates by saliva and distinct sites of oral cavity and is affected by risky behaviors (smoking, drinking and betel quid chewing) and individuals’ oral health condition. To characterize the disturbances in the oral microbial population mainly due to oral tumorigenicity, we profiled the bacteria within the surface of OSCC lesion and its contralateral normal tissue from discovery (n = 74) and validation (n = 42) cohorts of male patients with cancers of the buccal mucosa. Significant alterations in the bacterial diversity and relative abundance of specific oral microbiota (most profoundly, an enrichment for genus Fusobacterium and the loss of genus Streptococcus in the tumor sites) were identified. Functional prediction of oral microbiome shown that microbial genes related to the metabolism of terpenoids and polyketides were differentially enriched between the control and tumor groups, indicating a functional role of oral microbiome in formulating a tumor microenvironment via attenuated biosynthesis of secondary metabolites with anti-cancer effects. Furthermore, the vast majority of microbial signatures detected in the discovery cohort was generalized well to the independent validation cohort, and the clinical validity of these OSCC-associated microbes was observed and successfully replicated. Overall, our analyses reveal signatures (a profusion of Fusobacterium nucleatum CTI-2 and a decrease in Streptococcus pneumoniae) and functions (decreased production of tumor-suppressive metabolites) of oral microbiota related to oral cancer.

scholarly journals Microbial Population Changes during Bioremediation of an Experimental Oil Spill

1999 ◽  
Vol 65 (8) ◽  
pp. 3566-3574 ◽  
Author(s):  
Sarah J. MacNaughton ◽  
John R. Stephen ◽  
Albert D. Venosa ◽  
Gregory A. Davis ◽  
Yun-Juan Chang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Oil Spill ◽  
Phospholipid Fatty Acid ◽  
Community Structures ◽  
Gram Negative ◽  
Dgge Analysis ◽  
16S Rdna Pcr ◽  
Microbial Community Structures ◽  
Plfa Analysis

ABSTRACT Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria andFlexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

scholarly journals Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

2017 ◽  
Vol 312 (4) ◽  
pp. G327-G339 ◽  
Author(s):  
Rebecca L. Knoll ◽  
Kristoffer Forslund ◽  
Jens Roat Kultima ◽  
Claudius U. Meyer ◽  
Ulrike Kullmer ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Virulence Genes ◽  
Metagenomic Sequencing ◽  
Fecal Microbiome ◽  
Microbial Dysbiosis ◽  
Healthy Siblings ◽  
Inflammatory Bowel ◽  
Sibling Study

Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn’s disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. In addition, lifetime antibiotic intake was retrospectively determined. Species richness and diversity were significantly reduced in UC patients compared with control [Mann-Whitney U-test false discovery rate (MWU FDR) = 0.011]. In UC, bacteria positively influencing gut homeostasis, e.g., Eubacterium rectale and Faecalibacterium prausnitzii, were significantly reduced in abundance (MWU FDR = 0.05). Known pathobionts like Escherichia coli were enriched in UC patients (MWU FDR = 0.084). Moreover, E. coli abundance correlated positively with that of several virulence genes (SCC > 0.65, FDR < 0.1). A shift toward antibiotic-resistant taxa in both IBD groups distinguished them from controls [MWU Benjamini-Hochberg-Yekutieli procedure (BY) FDR = 0.062 in UC, MWU BY FDR = 0.019 in CD). The collected results confirm a microbial dysbiosis in pediatric UC, and to a lesser extent in CD patients, replicating associations found previously using different methods. Taken together, these observations suggest microbiotal remodeling therapy from family donors, at least for children with UC, as a viable option. NEW & NOTEWORTHY In this sibling study, prior reports of microbial dysbiosis in IBD patients from 16S rRNA sequencing was verified using deep shotgun sequencing and augmented with insights into the abundance of bacterial virulence genes and bacterial antibiotic resistance determinants, seen against the background of data on the specific antibiotic intake of each of the study participants. The observed dysbiosis, which distinguishes patients from siblings, highlights such siblings as potential donors for microbiotal remodeling therapy in IBD.

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-9
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Bacterial Species ◽  
Abundant Species ◽  
Rrna Gene ◽  
Core Microbiome ◽  
The Core ◽  
Severe Periodontal Disease ◽  
Healthy Dogs ◽  
V3 Region

Abstract OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

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