scholarly journals Similarity of salivary microbiome in parents and adult children

2019 ◽  
Author(s):  
Kati Sundström ◽  
Pashupati P Mishra ◽  
Mikko J Pyysalo ◽  
Terho Lehtimäki ◽  
Pekka J Karhunen ◽  
...  
Keyword(s):  
Adult Children ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Genus Level ◽  
Abundant Genus ◽  
Dna Profiles

Background: Human saliva contains approximately 700 bacterial species but the relatedness of salivary bacteria from parents to adult children is not investigated in humans. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between adult parent-off-spring pairs using 16S rRNA gene amplicon sequencing. Results: The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13 % of the variance between individuals’ bacterial communities (R2=0.13; P=0.001). Mothers shared more OTUs with their adult children compared to fathers, but this linkage seemed to be weaker in the family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between the families, which accounted for 31 % of the total identified genus level OTUs Conclusions: Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. Our results suggest implicitly that a similarity in oral microbiome between parent-child pairs is present, but may change over time.

scholarly journals Similarity of salivary microbiome in parents and adult children

2019 ◽  
Author(s):  
Kati Sundström ◽  
Pashupati P Mishra ◽  
Mikko J Pyysalo ◽  
Terho Lehtimäki ◽  
Pekka J Karhunen ◽  
...  
Keyword(s):  
Adult Children ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Genus Level ◽  
Abundant Genus ◽  
Dna Profiles

Background: Human saliva contains approximately 700 bacterial species but the relatedness of salivary bacteria from parents to adult children is not investigated in humans. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between adult parent-off-spring pairs using 16S rRNA gene amplicon sequencing. Results: The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13 % of the variance between individuals’ bacterial communities (R2=0.13; P=0.001). Mothers shared more OTUs with their adult children compared to fathers, but this linkage seemed to be weaker in the family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between the families, which accounted for 31 % of the total identified genus level OTUs Conclusions: Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. Our results suggest implicitly that a similarity in oral microbiome between parent-child pairs is present, but may change over time.

scholarly journals Similarity of salivary microbiome in parents and adult children

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8799 ◽  
Author(s):  
Kati Sundström ◽  
Pashupati P. Mishra ◽  
Mikko J. Pyysalo ◽  
Terho Lehtimäki ◽  
Pekka J. Karhunen ◽  
...  
Keyword(s):  
Adult Children ◽  
Bacterial Communities ◽  
Nuclear Family ◽  
Bacterial Species ◽  
Large Family ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Genus Level

Background Human saliva contains approximately 700 bacterial species. It has been reported that the salivary microbiome of a large family of closely related individuals consisting of multiple households is similar but the relatedness of salivary bacteria between generations of parents and their children has not yet been investigated. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between grandparents and their first daughter generations (F1) using 16S rRNA gene amplicon sequencing. Results The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13% of the variance between individuals’ bacterial communities (R2 = 0.13; P = 0.001). Mothers shared more OTUs with adult children compared to fathers, but this linkage seemed to be weaker in the nuclear family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between families, which accounted for 31% of the total identified genus level OTUs. Conclusions Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. The observed similarity in oral microbiome between parent–child pairs seemed to weaken over time. We suggest that our analysis approach is suitable for relatedness study of multigenerational salivary bacteria microbiome.

scholarly journals Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

2021 ◽  
Vol 12 ◽  
Author(s):  
Kuleshwar Prasad Sahu ◽  
Asharani Patel ◽  
Mukesh Kumar ◽  
Neelam Sheoran ◽  
Sahil Mehta ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rice Blast ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Rice Cultivar ◽  
Disease Suppression ◽  
Blast Disease ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Microbiological Methods

Phyllosphere—the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members Pantoea, Enterobacter, Pseudomonas, and Erwinia on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.

scholarly journals Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

2021 ◽  
Vol 9 (8) ◽  
pp. 1657
Author(s):  
Anders Esberg ◽  
Linda Johansson ◽  
Ingegerd Johansson ◽  
Solbritt Rantapää Dahlqvist
Keyword(s):  
Rheumatoid Arthritis ◽  
Early Onset ◽  
Amplicon Sequencing ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Disease Manifestation ◽  
Periodontal Status ◽  
Quality Register

Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

scholarly journals The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

2017 ◽  
Vol 1 (3) ◽  
pp. 158-168 ◽  
Author(s):  
Kristi Gdanetz ◽  
Frances Trail
Keyword(s):  
Bacterial Communities ◽  
Management Strategy ◽  
Crop Yields ◽  
Management Strategies ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

Temporal variation in soil bacterial communities can be confounded with spatial variation

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Syrie M Hermans ◽  
Hannah L Buckley ◽  
Fiona Curran-Cournane ◽  
Matthew Taylor ◽  
Gavin Lear
Keyword(s):  
Temporal Variation ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Spatial Distance ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Causal Processes ◽  
Fundamental Understanding ◽  
Soil Bacterial ◽  
Indigenous Forest

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P &lt; 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (&lt;1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

scholarly journals Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 748 ◽  
Author(s):  
Jin-Young Lee ◽  
Mohamed Mannaa ◽  
Yunkyung Kim ◽  
Jehun Kim ◽  
Geun-Tae Kim ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Stool Samples ◽  
Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

scholarly journals Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michael J. LaMonte ◽  
Robert J. Genco ◽  
Michael J. Buck ◽  
Daniel I. McSkimming ◽  
Lu Li ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Relative Abundance ◽  
Multiple Testing ◽  
Statistical Significance ◽  
Bacterial Species ◽  
Age Groups ◽  
Later Life ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Age Range

Abstract Background The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood. Methods The 16S rRNA gene of subgingival plaque in 1219 women, aged 53–81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method. Results Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = − 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50–59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older. Conclusions We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.

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